Contacts of the strand formed by residues 155 - 163 (chain B) in PDB entry 3HQL
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 LEU 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B TRP 3.5 1.9 - - - +
37B THR* 3.4 1.9 - - - -
38B ILE* 2.8 44.2 + - + +
41B PHE* 3.7 37.0 - - + +
71B VAL* 5.7 0.2 - - + -
84B LEU* 3.8 20.9 - - + -
106B ILE* 4.0 19.5 - - + -
142B LEU* 3.9 28.0 - - + -
149B LEU 4.1 2.2 - - - +
150B LEU* 3.7 12.1 - - + +
153B ASP 4.2 0.4 + - - -
154B LYS* 1.3 73.1 - - - +
156B THR* 1.3 63.1 + - - +
157B LEU* 4.1 28.5 - - + -
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Residues in contact with THR 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B MET* 3.4 40.4 - - + -
36B TRP 3.5 2.9 - - - +
37B THR* 3.8 20.0 + - - +
106B ILE* 3.5 7.1 - - - +
107B LEU* 2.9 54.0 + - + -
149B LEU 4.9 1.0 + - - -
151B PRO* 6.2 0.5 - - - +
154B LYS* 3.9 6.8 + - - +
155B LEU* 1.3 77.5 + - - +
157B LEU* 1.3 59.5 + - - +
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Residues in contact with LEU 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B TYR 4.6 0.2 - - - -
35B MET* 3.4 6.2 - - - +
36B TRP* 2.8 68.3 + - + +
38B ILE* 4.1 14.8 - - + -
69B LEU* 5.1 5.4 - - + -
71B VAL* 5.0 5.6 - - + -
84B LEU* 5.6 2.0 - - + -
86B LEU* 4.1 24.9 - - + -
104B PHE* 6.4 0.2 - - + -
105B SER 3.4 4.9 - - - +
106B ILE* 3.9 26.2 - - + -
136B PHE* 4.2 14.4 - - + -
155B LEU* 4.1 25.4 - - + -
156B THR* 1.3 75.1 - - - +
158B PHE* 1.3 60.8 + - - +
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Residues in contact with PHE 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B SER* 3.5 33.0 - - - -
34B TYR 3.6 17.7 - - - -
35B MET* 4.0 14.6 - - + -
69B LEU* 5.6 0.4 - - - -
103B LYS 3.8 0.9 - - - +
104B PHE* 3.3 4.8 - - - +
105B SER* 2.9 42.5 + - - +
107B LEU* 3.8 22.4 - - + -
113B GLU* 3.6 28.3 - - + -
157B LEU* 1.3 76.2 - - - +
159B CYS* 1.3 58.1 + - - +
160B GLU* 3.4 30.2 - - + +
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Residues in contact with CYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B SER* 3.1 8.3 - - - -
34B TYR* 2.9 36.6 + - + +
57B PHE* 4.6 3.8 - - - -
69B LEU* 3.8 29.6 - - + -
88B LEU* 4.2 4.7 - - - -
102B PHE* 4.9 0.2 - - - -
103B LYS 3.3 4.9 - - - -
104B PHE* 3.4 32.8 - - + -
158B PHE* 1.3 74.3 - - - +
160B GLU* 1.3 65.0 + - - +
161B VAL* 3.6 25.8 - - - -
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Residues in contact with GLU 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LYS* 4.2 27.0 + - - +
32B PHE 3.4 7.0 - - - +
33B SER* 4.3 3.6 - - - -
102B PHE* 3.2 4.7 - - - +
103B LYS* 2.9 59.2 + - + +
105B SER* 4.8 0.5 + - - -
113B GLU* 3.0 28.6 - - - +
158B PHE* 3.4 31.9 - - + +
159B CYS* 1.3 73.6 - - - +
161B VAL* 1.3 63.4 + - - +
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Residues in contact with VAL 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B VAL 4.4 0.2 - - - -
31B LYS* 3.3 6.7 - - - +
32B PHE* 2.8 72.8 + - + +
33B SER* 5.9 0.2 - - - -
57B PHE* 4.7 3.1 - - + -
67B TRP* 4.6 4.0 - - + -
88B LEU* 3.7 25.4 - - + -
100B ALA* 4.0 19.1 - - + -
101B LYS 3.4 10.1 - - - +
102B PHE* 4.5 0.7 - - + -
159B CYS* 3.6 22.9 - - - +
160B GLU* 1.3 79.9 - - - +
162B SER* 1.3 66.1 + - - +
163B VAL* 4.5 2.0 - - + -
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Residues in contact with SER 162 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 5.7 5.4 - - - -
30B VAL 3.3 7.6 - - - -
31B LYS* 4.3 17.5 - - - -
100B ALA* 3.3 2.9 - - - -
101B LYS* 2.9 53.3 + - - +
161B VAL* 1.3 74.5 - - - +
163B VAL* 1.3 63.9 + - - +
164B VAL 4.1 0.7 + - - -
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Residues in contact with VAL 163 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LYS 3.9 0.9 - - - +
29B VAL* 3.7 3.4 - - - +
30B VAL* 2.8 46.9 + - + +
32B PHE* 4.3 15.3 - - + -
65B LEU* 5.3 5.8 - - + -
67B TRP* 4.3 18.4 - - + -
98B VAL* 4.7 15.5 - - + -
99B ARG 3.7 13.2 - - - +
100B ALA* 4.0 16.8 - - + -
161B VAL* 4.5 0.7 - - + -
162B SER* 1.3 76.8 - - - +
164B VAL* 1.3 65.4 + - - +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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