Contacts of the strand formed by residues 144 - 157 (chain C) in PDB entry 3DOY
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 LYS 144 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111C ILE* 3.9 35.8 - - + +
140C GLN* 3.2 5.9 - - - -
141C VAL* 3.1 40.4 + - - +
142C ASP* 3.3 15.0 - - - +
143C GLY* 1.3 78.5 - - - +
145C VAL* 1.3 64.2 + - - +
146C VAL* 3.2 3.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 145 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C ARG* 3.9 32.6 - - - +
111C ILE* 4.1 9.7 - - - +
138C THR* 4.0 19.7 - - + +
139C ALA 3.8 4.0 - - - -
140C GLN* 4.0 16.4 - - + +
143C GLY 3.9 2.2 + - - +
144C LYS* 1.3 69.9 - - - +
146C VAL* 1.3 61.2 + - - +
147C ALA 3.6 24.5 - - - +
148C GLU* 4.5 6.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 146 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 4.7 6.5 - - + -
109C PHE* 3.7 3.3 - - - +
110C ARG* 3.0 23.3 + - - -
111C ILE* 2.7 51.6 + - + +
112C PRO 5.4 0.4 - - - +
113C VAL* 3.4 23.3 - - + -
119C LEU* 5.1 1.3 - - + -
139C ALA* 2.8 14.7 + - + +
141C VAL* 3.6 30.3 - - + +
144C LYS* 3.6 15.0 - - + +
145C VAL* 1.3 74.9 - - - +
147C ALA* 1.3 61.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 147 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 4.3 11.9 - - + -
71C VAL* 6.2 0.9 - - + -
74C MET* 5.2 2.9 - - - -
107C VAL* 5.8 0.2 - - + -
108C LYS 3.1 14.4 - - - +
109C PHE* 3.8 21.1 - - + -
110C ARG* 4.6 1.3 - - - +
138C THR* 3.2 9.7 - - - +
139C ALA* 3.0 36.3 + - + +
145C VAL* 3.6 6.5 - - - +
146C VAL* 1.3 85.0 - - + +
148C GLU* 1.3 63.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 148 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C MET* 4.6 2.5 - - - -
106C LYS* 3.8 9.5 - - - +
107C VAL* 3.1 23.4 - - - +
108C LYS* 3.0 36.9 + - + +
110C ARG* 3.3 31.0 + - - -
137C GLY 3.3 14.1 - - - +
138C THR* 3.7 12.2 - - + +
145C VAL* 4.5 7.8 - - - +
147C ALA* 1.3 77.2 - - - +
149C ALA* 1.3 65.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 149 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL* 4.6 7.0 - - + -
74C MET* 4.1 19.2 - - + +
105C ASP 3.7 6.1 - - - -
106C LYS* 3.8 3.1 - - - -
107C VAL* 3.4 23.1 - - + -
123C LEU* 5.2 0.7 - - - +
136C GLY* 3.3 2.6 - - - -
137C GLY 3.1 31.0 + - - +
148C GLU* 1.3 78.0 - - - +
150C GLU* 1.3 68.7 + - - +
151C LEU* 4.7 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 150 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ILE* 3.4 0.9 - - - +
105C ASP* 2.9 43.9 + - + +
106C LYS* 3.8 35.1 + - + +
126C LEU* 4.1 20.9 - - + +
134C GLN* 3.9 17.3 + - + +
135C VAL 3.3 9.0 - - - +
136C GLY* 4.1 1.3 - - - -
149C ALA* 1.3 75.1 - - - +
151C LEU* 1.3 76.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 151 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C VAL* 3.9 16.4 - - + +
74C MET* 4.0 10.3 - - + +
75C ALA* 3.4 42.0 - - + +
101C PHE* 3.8 10.8 - - + -
103C THR* 3.4 6.1 - - - +
104C ILE* 3.4 33.2 - - + -
123C LEU* 4.4 4.3 - - + -
133C TRP 3.8 0.2 - - - +
134C GLN* 3.3 5.9 - - - +
135C VAL* 2.7 60.1 + - + +
149C ALA* 4.7 5.4 - - + +
150C GLU* 1.3 90.6 - - - +
152C LYS* 1.3 60.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 152 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101C PHE* 3.6 5.4 - - - -
102C MET* 2.8 51.1 + - - +
103C THR* 3.0 36.6 + - - +
132C ILE* 3.7 30.0 - - + +
133C TRP 3.3 6.3 - - - +
134C GLN* 4.3 20.0 - - + +
151C LEU* 1.3 73.9 - - - +
153C ALA* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 153 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99C VAL* 3.5 22.9 - - + -
100C TYR 3.0 13.5 - - - +
101C PHE* 3.6 20.0 - - + -
102C MET* 4.2 5.4 - - - +
132C ILE* 3.4 5.9 - - - +
133C TRP* 2.8 40.8 + - + +
135C VAL* 6.4 0.4 - - + -
152C LYS* 1.3 76.2 - - - +
154C MET* 1.3 59.8 + - - +
155C ILE* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 154 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98C ILE 3.7 0.9 - - - +
99C VAL* 3.3 4.0 - - - -
100C TYR* 2.7 59.5 + - + +
102C MET* 3.8 32.7 - - + -
131C MET* 3.3 11.0 - - + +
132C ILE* 3.7 20.6 - - + -
153C ALA* 1.3 75.4 - - - +
155C ILE* 1.3 74.3 + - - +
156C ALA* 5.0 4.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 155 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ALA* 3.9 18.4 - - + -
83C PHE* 4.6 4.7 - - + +
86C LEU* 3.5 18.4 - - + -
87C TRP* 4.2 25.6 - - + -
97C LYS* 4.9 5.8 - - + -
98C ILE 3.6 4.3 - - - +
99C VAL* 4.1 20.6 - - + -
131C MET* 2.9 51.3 + - + +
133C TRP* 3.4 32.3 - - + +
153C ALA* 6.0 0.2 - - + -
154C MET* 1.3 78.4 - - - +
156C ALA* 1.3 71.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 156 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C LYS* 3.4 14.5 - - - +
98C ILE* 3.0 32.5 + - + -
100C TYR* 4.2 26.2 - - + -
131C MET* 4.6 6.3 - - - -
154C MET* 5.0 6.3 - - - -
155C ILE* 1.3 78.0 - - - +
157C GLU* 1.3 65.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 157 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C THR* 2.4 36.6 + - - +
97C LYS* 2.8 27.4 + - - +
98C ILE* 4.0 12.1 - - - +
100C TYR* 5.3 0.5 + - - -
156C ALA* 1.3 79.7 - - - +
158C ARG* 1.3 69.2 + - - +
----------------------------------------------------------
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