Contacts of the helix formed by residues 111 - 128 (chain B) in PDB entry 3U8Z
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 GLN 111 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLY 2.7 30.9 + - - -
56B LEU* 3.8 3.9 - - - +
57B ARG* 2.7 58.2 + - - +
58B GLU* 3.0 32.6 + - + +
109B LEU 4.1 0.5 - - - +
110B VAL* 1.4 79.5 - - + +
112B GLU* 1.3 61.9 + - - +
113B ILE* 4.1 12.5 - - + +
114B THR* 2.9 23.1 - - + +
115B GLN* 3.3 10.2 + - - +
200B ARG* 4.6 3.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B VAL 4.0 1.4 + - - -
111B GLN* 1.3 71.1 - - - +
113B ILE* 1.4 55.6 + - - +
115B GLN* 3.2 18.8 + - - +
116B HIS* 2.7 38.4 + - + +
198B ARG* 2.8 36.1 + - - -
200B ARG* 3.3 19.6 - - + +
201B ASP* 2.8 29.3 + - - +
204B GLU* 4.9 3.1 - - - +
55D GLY* 4.0 10.4 - - - +
57D ARG* 3.2 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B LEU* 3.6 35.7 - - + +
55B GLY 4.4 0.2 - - - +
56B LEU* 3.8 22.0 - - + -
111B GLN* 4.1 18.4 - - + +
112B GLU* 1.4 76.2 - - - +
114B THR* 1.3 53.9 + - - +
116B HIS* 3.2 10.0 + - + +
117B LEU* 2.8 63.7 + - + +
52D ARG 4.2 4.9 - - - +
53D THR 3.2 28.7 - - - +
54D LEU 4.7 0.2 - - - +
55D GLY* 4.0 20.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 3.9 18.8 - - - -
58B GLU* 2.8 30.9 + - - +
61B PHE* 4.2 3.8 - - - -
62B PHE* 3.7 23.1 - - - -
109B LEU* 3.6 25.5 - - + +
111B GLN* 2.9 27.8 - - + +
113B ILE* 1.3 79.4 - - - +
115B GLN* 1.3 54.2 + - - +
117B LEU* 3.3 1.3 + - - +
118B PHE* 2.9 38.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B LEU* 4.0 15.0 + - + +
111B GLN 3.6 10.3 + - - +
112B GLU* 3.2 18.8 + - - +
114B THR* 1.3 79.8 - - - +
116B HIS* 1.4 55.6 + - - +
119B PHE* 3.0 29.5 + - - +
200B ARG* 4.8 16.0 - - - +
201B ASP 3.0 28.2 + - - +
202B GLU* 5.1 3.4 + - - +
204B GLU* 3.0 24.9 - - + +
205B MET* 3.6 43.9 - - + +
208B LEU* 3.6 6.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ASP* 2.7 38.8 + - - -
112B GLU* 2.7 22.5 + - + +
113B ILE* 3.4 12.6 - - + +
115B GLN* 1.4 69.9 - - - +
117B LEU* 1.3 64.9 + - - +
119B PHE* 3.3 3.2 + + - +
120B LEU* 3.1 45.7 + - + +
204B GLU* 2.7 37.4 + - - +
52D ARG* 3.4 47.2 + - + +
55D GLY* 6.2 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B THR* 4.5 19.1 - - + -
29B MET* 4.2 14.2 - - + +
30B ASP* 3.8 21.1 - - - +
54B LEU* 4.5 7.4 - - + -
56B LEU* 4.7 4.9 - - + -
62B PHE* 4.0 22.9 - - + -
96B PHE* 3.8 31.9 - - + +
113B ILE* 2.8 46.5 + - + +
114B THR* 3.8 4.3 - - - +
116B HIS* 1.3 71.7 - - - +
118B PHE* 1.4 61.9 + - - +
120B LEU* 3.6 4.3 + - - +
121B GLN* 3.2 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B PHE* 3.7 22.7 - + + -
62B PHE* 3.7 17.5 - + - -
98B ALA* 3.5 20.9 - - + -
100B PHE 3.2 27.4 - - - -
101B TYR* 3.7 22.4 - + - -
102B PRO* 3.6 22.0 - - + -
109B LEU* 3.7 34.5 - - + -
114B THR* 2.9 26.2 + - - +
115B GLN 4.0 1.1 - - - +
117B LEU* 1.4 72.7 - - - +
119B PHE* 1.3 66.3 - - - +
121B GLN* 3.3 4.4 + - + -
122B VAL* 2.9 32.4 + - + +
208B LEU* 3.9 9.2 - - + -
217B TYR* 4.8 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLN 3.0 21.5 + - - +
116B HIS 3.3 3.3 + - - +
118B PHE* 1.3 75.4 - - - +
120B LEU* 1.3 70.5 + - + +
122B VAL* 4.0 0.7 - - - +
123B LYS* 2.9 62.1 + - + +
145B ALA* 4.1 7.9 - - - -
148B ALA* 3.7 22.2 - - + -
203B ALA 5.0 0.2 - - - -
204B GLU* 3.2 46.2 - - + +
207B TYR* 3.4 51.2 - + + -
208B LEU* 3.8 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET* 3.4 40.1 - - + +
30B ASP* 3.5 35.7 - - - +
116B HIS* 3.1 34.9 + - + +
117B LEU* 4.1 2.0 - - - +
119B PHE* 1.3 92.9 - - + +
121B GLN* 1.3 65.0 + - - +
123B LYS* 3.9 17.1 + - - +
124B LYS* 3.1 18.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B MET* 3.9 15.4 - - + +
62B PHE* 5.3 1.6 - - - -
97B LEU* 3.5 28.5 - - + +
98B ALA* 2.8 52.4 + - - +
101B TYR* 3.0 24.1 + - - +
117B LEU 3.2 17.0 + - - +
118B PHE* 3.3 5.1 + - + +
120B LEU* 1.3 80.0 - - - +
122B VAL* 1.4 62.1 + - + +
124B LYS* 3.5 5.5 + - - +
125B GLN* 3.4 33.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TYR* 4.0 20.2 - - + -
118B PHE* 2.9 23.1 + - + +
119B PHE 4.1 0.7 - - - +
121B GLN* 1.4 71.4 - - + +
123B LYS* 1.4 60.1 + - - +
125B GLN* 3.1 12.7 + - - +
126B ILE* 3.0 30.4 + - + +
131B ILE* 4.3 7.6 - - + -
207B TYR* 4.4 3.1 - - + -
208B LEU* 3.9 15.7 - - + -
211B ALA* 3.6 30.5 - - + -
217B TYR* 3.6 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PHE* 2.9 56.1 + - + +
120B LEU* 3.9 17.8 + - - +
122B VAL* 1.4 75.9 - - - +
124B LYS* 1.4 57.9 + - - +
126B ILE* 3.1 2.4 + - - +
127B LEU* 2.9 57.1 + - + +
145B ALA* 3.9 19.7 - - + -
207B TYR* 3.4 24.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASP* 5.7 6.9 + - - +
289A LYS* 5.1 9.6 - - - +
291A ARG* 5.7 3.9 - - - +
29B MET* 3.9 20.5 - - + +
120B LEU 3.1 18.4 + - - +
121B GLN 3.7 6.1 - - - +
122B VAL 3.3 0.2 - - - -
123B LYS* 1.4 75.5 - - - +
125B GLN* 1.3 58.9 + - + +
127B LEU* 3.8 6.1 - - - +
128B ASP* 2.9 59.8 + - - +
130B LYS* 5.0 8.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B TYR* 3.0 32.2 + - - -
121B GLN* 3.4 28.4 + - - +
122B VAL* 3.1 11.8 + - - +
124B LYS* 1.3 75.8 - - + +
126B ILE* 1.4 62.5 + - - +
128B ASP* 4.5 1.3 - - - -
129B GLU 3.2 0.9 + - - -
130B LYS* 2.9 51.7 + - + -
131B ILE* 3.2 37.6 + - + +
218B GLY 5.4 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ARG* 3.8 14.8 + - - +
231A GLU* 4.3 3.1 - - - +
122B VAL* 3.0 24.9 + - + +
123B LYS 3.1 6.7 + - - +
125B GLN* 1.4 75.5 - - - +
127B LEU* 1.3 70.7 + - + +
129B GLU* 3.2 14.2 + - - +
131B ILE* 3.9 25.0 - - + +
133B CYS* 4.5 10.8 - - + -
138B SER* 5.8 3.1 - - - +
141B LEU* 3.9 22.7 - - + -
207B TYR* 3.5 21.8 - - + +
211B ALA* 4.7 3.6 - - + -
214B LEU* 3.6 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A ARG* 2.6 30.3 + - - +
288A SER* 3.6 18.6 + - - +
123B LYS* 2.9 47.3 + - + +
124B LYS* 4.0 5.6 - - + +
126B ILE* 1.3 85.3 - - + +
128B ASP* 1.4 61.2 + - - +
129B GLU* 3.2 1.8 - - - +
142B ALA* 6.4 2.0 - - + -
207B TYR* 5.2 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ALA* 3.7 13.2 - - - +
288A SER* 4.6 8.5 + - - -
289A LYS* 3.3 33.0 + - - +
124B LYS* 2.9 44.6 + - - +
125B GLN 4.2 0.9 - - - +
127B LEU* 1.4 75.7 - - - +
129B GLU* 1.3 67.4 - - - +
130B LYS* 3.5 40.1 + - + +
----------------------------------------------------------
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