Contacts of the helix formed by residues 113 - 134 (chain C) in PDB entry 3UDB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER 113 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ARG* 4.0 1.1 + - - +
112C PHE* 1.3 77.6 - - - +
114C GLU* 1.3 65.1 + - - +
115C ASP* 3.5 7.7 + - - +
116C GLU* 3.1 28.2 + - - +
117C ALA* 3.0 19.4 + - - +
211C LEU* 4.7 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 114 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C PHE 3.8 0.8 + - - -
113C SER* 1.3 72.6 - - - +
115C ASP* 1.3 58.5 + - - +
117C ALA* 3.1 4.0 + - - +
118C ARG* 2.9 37.9 + - - +
211C LEU* 3.9 16.5 - - + +
245C HIS 4.3 4.4 - - - +
246C ILE* 3.3 12.0 - - + -
247C SER* 2.6 49.8 + - - -
250C CYS* 4.0 4.5 - - - -
276C TRP* 2.7 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 115 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C SER* 3.2 7.8 + - - +
114C GLU* 1.3 78.1 - - - +
116C GLU* 1.3 58.6 + - - +
118C ARG* 2.7 35.0 + - - +
119C PHE* 3.1 25.5 + - - +
279C LYS* 4.1 5.7 + - - -
280C ASN* 4.1 15.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C ARG* 2.3 36.6 + - - -
109C ALA* 6.0 0.3 - - - +
112C PHE* 3.9 28.1 - - + -
113C SER* 3.1 24.6 + - - +
115C ASP* 1.3 78.6 - - - +
117C ALA* 1.3 64.0 + - - +
119C PHE* 3.2 22.5 + - + +
120C PHE* 3.3 21.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C PHE* 4.2 4.6 - - + +
113C SER 3.0 13.9 + - - +
114C GLU 3.6 7.2 - - - +
116C GLU* 1.3 77.6 - - - +
118C ARG* 1.3 58.5 + - - +
120C PHE 3.3 0.5 + - - -
121C PHE* 2.9 31.9 + - - +
207C LEU* 4.4 5.2 - - + -
210C MET* 3.4 35.1 - - + +
211C LEU* 3.7 23.6 - - + -
276C TRP* 4.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 118 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114C GLU* 2.9 21.8 + - - +
115C ASP* 2.7 41.9 + - - +
116C GLU 3.2 0.2 - - - -
117C ALA* 1.3 76.7 - - - +
119C PHE* 1.3 56.5 + - - +
121C PHE* 4.3 0.4 - - - -
122C GLN* 3.0 48.4 + - + +
276C TRP* 3.0 75.0 + - + +
277C PHE 4.9 0.2 - - - +
279C LYS* 3.2 60.7 + - - +
280C ASN* 5.1 4.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 119 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C ASP 3.1 14.4 + - - +
116C GLU* 3.3 14.4 - - + +
117C ALA 3.2 0.2 - - - -
118C ARG* 1.3 78.5 - - - +
120C PHE* 1.3 83.7 + + - +
122C GLN* 4.0 11.9 - - - +
123C GLN* 3.2 45.8 + - + +
153C ALA* 3.5 38.1 - - + -
154C PRO* 3.4 12.6 - - + -
155C ARG* 3.7 21.3 - - - -
282C PRO* 6.0 6.1 - - + -
285C LEU* 5.2 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 120 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LEU* 4.3 7.0 - - + -
105C ARG* 4.1 7.9 - - - -
112C PHE* 3.6 30.7 - + - -
116C GLU* 3.3 35.9 + - + -
119C PHE* 1.3 87.6 - + - +
121C PHE* 1.3 60.5 + - - +
122C GLN 3.3 0.4 - - - -
123C GLN* 3.2 12.2 + - - +
124C LEU* 2.9 29.1 + - - +
148C LEU* 3.3 30.7 - - + -
154C PRO* 3.4 39.5 - - + -
156C LEU* 4.2 14.2 - - + +
210C MET* 3.6 20.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 121 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C ALA 2.9 18.9 + - - +
118C ARG* 4.0 5.4 - - - +
120C PHE* 1.3 74.7 - - - +
122C GLN* 1.3 64.4 + - + +
124C LEU* 3.6 12.6 - - + +
125C ILE* 3.0 52.5 + - + +
203C CYS* 3.5 30.1 - - + -
207C LEU* 3.8 30.1 - - + -
210C MET* 4.0 7.3 - - + +
253C LEU* 4.0 11.9 - - + -
257C ILE* 4.4 15.9 - - + -
271C ILE* 4.0 17.0 - - + -
276C TRP* 3.8 17.7 - + + -
277C PHE* 4.0 12.1 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 122 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ARG* 3.0 40.4 + - + +
119C PHE* 4.0 9.9 - - - +
121C PHE* 1.3 77.3 - - + +
123C GLN* 1.3 62.3 + - - +
125C ILE* 3.9 1.0 - - - +
126C SER* 3.0 24.3 + - - -
277C PHE* 2.9 45.2 + - + +
279C LYS 3.2 20.4 + - - -
280C ASN* 3.9 3.9 - - - +
281C LEU* 3.4 20.3 - - + +
282C PRO* 3.7 14.2 - - - +
285C LEU* 3.5 17.2 - - + +
286C MET* 3.7 3.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 123 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ASN* 3.0 34.4 + - - +
119C PHE* 3.2 55.7 + - + +
120C PHE* 3.2 10.3 + - - +
122C GLN* 1.3 76.3 - - - +
124C LEU* 1.3 62.9 + - - +
126C SER* 3.2 1.0 + - - -
127C GLY* 2.8 21.3 + - - -
154C PRO 3.9 2.8 + - - -
155C ARG* 3.4 28.3 + - - +
156C LEU* 2.8 35.7 + - + -
285C LEU* 3.8 11.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LEU* 6.3 1.3 - - + -
120C PHE 2.9 19.8 + - - +
121C PHE* 3.3 15.9 + - + +
123C GLN* 1.3 72.6 - - - +
125C ILE* 1.3 58.7 + - + +
127C GLY* 3.3 1.0 + - - -
128C VAL* 3.0 45.6 + - + +
143C LEU* 4.8 7.0 - - + +
146C THR* 4.5 15.0 - - + -
156C LEU* 3.6 23.7 - - + +
158C ILE* 4.4 9.7 - - + +
203C CYS* 3.9 35.0 - - + +
206C THR* 3.6 27.6 - - + +
210C MET* 6.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 125 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C PHE* 3.0 52.7 + - + +
124C LEU* 1.3 74.4 - - + +
126C SER* 1.3 62.6 + - - +
128C VAL* 4.0 2.2 - - - +
129C SER* 2.9 28.8 + - - -
203C CYS* 4.1 22.2 - - + -
268C ILE* 4.0 37.6 - - + +
271C ILE* 4.3 15.0 - - + -
272C ARG* 4.2 10.5 - - + -
277C PHE* 3.7 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 126 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C HIS* 2.9 22.7 + - - -
122C GLN 3.0 12.7 + - - -
123C GLN 3.6 2.5 - - - -
125C ILE* 1.3 78.3 - - - +
127C GLY* 1.3 61.5 + - - +
129C SER* 3.8 4.1 - - - -
130C TYR* 3.2 22.3 + - - +
272C ARG* 4.9 0.4 + - - +
285C LEU* 3.4 16.0 - - - +
286C MET* 1.7 47.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 127 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C HIS* 3.9 18.6 - - - -
76C ASN* 4.2 8.5 - - - -
77C ILE* 4.4 6.5 - - - +
123C GLN 2.8 15.4 + - - -
124C LEU 3.8 1.3 - - - -
126C SER* 1.3 76.9 + - - +
128C VAL* 1.3 57.0 + - - +
130C TYR* 3.3 5.5 + - - +
131C ALA* 3.0 26.5 + - - +
158C ILE* 4.3 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 128 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C LEU* 3.0 25.0 + - + +
125C ILE* 4.0 4.0 - - - +
127C GLY* 1.3 74.3 - - - +
129C SER* 1.3 65.5 + - - +
131C ALA* 3.3 6.9 + - - +
132C HIS* 3.0 49.8 + - + +
141C LEU* 5.3 6.1 - - + -
143C LEU* 3.9 34.1 - - + -
158C ILE* 4.4 5.8 - - + -
199C ASP* 4.7 7.6 - - + +
203C CYS* 4.1 12.3 - - - -
268C ILE* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 129 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C ILE 2.9 20.0 + - - -
126C SER 3.8 4.3 - - - -
128C VAL* 1.3 78.6 - - - +
130C TYR* 1.3 61.0 + - - +
132C HIS* 3.2 9.1 + - - +
133C ALA* 3.1 22.3 + - - +
268C ILE* 3.6 25.6 - - - +
272C ARG* 4.0 20.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 130 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C SER 3.7 8.7 + - - -
72C LEU* 4.1 21.5 - - + -
73C ARG* 3.1 39.2 + - - +
74C HIS* 3.7 33.2 - + + -
77C ILE* 4.4 8.3 - - + -
126C SER 3.2 11.8 + - - +
127C GLY 3.4 7.6 - - - +
129C SER* 1.3 76.4 + - - +
131C ALA* 1.3 71.2 + - - +
132C HIS 2.9 0.9 + - - -
133C ALA* 3.0 17.0 + - + +
134C MET* 3.2 32.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 131 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C LEU* 5.8 2.5 - - + -
77C ILE* 4.6 13.0 - - + -
127C GLY 3.0 13.3 + - - +
128C VAL* 3.3 6.7 + - - +
130C TYR* 1.3 86.2 - - - +
132C HIS* 1.3 63.7 + - + +
134C MET* 3.2 17.6 + - - +
135C GLN* 3.6 11.1 + - - +
141C LEU* 4.2 25.1 - - + -
158C ILE* 6.4 0.7 - - + -
160C ASP* 5.4 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 132 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128C VAL* 3.0 32.7 + - + +
129C SER* 3.3 11.4 - - - +
130C TYR 3.0 0.6 - - - -
131C ALA* 1.3 76.4 - - + +
133C ALA* 1.3 62.3 + - - +
134C MET 3.0 5.7 + - - -
135C GLN* 3.3 12.2 + - - +
141C LEU* 5.9 3.6 - - + -
196C LYS* 3.2 78.2 + - + +
199C ASP* 3.0 26.9 + - + -
268C ILE* 4.2 17.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 133 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129C SER 3.1 8.7 + - - +
130C TYR* 3.0 11.3 + - + +
132C HIS* 1.3 78.1 - - - +
134C MET* 1.3 64.2 + - - +
135C GLN 3.2 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 134 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C SER* 4.0 23.6 - - - +
72C LEU* 4.0 23.1 - - + -
130C TYR* 3.2 41.5 + - + +
131C ALA* 3.5 11.0 - - - +
132C HIS 3.0 1.0 - - - -
133C ALA* 1.3 83.6 - - - +
135C GLN* 1.3 72.2 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il