Contacts of the strand formed by residues 30 - 38 (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 VAL 30 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28B LYS 5.1 5.8 - - - +
29B VAL* 1.3 83.4 - - - +
31B LYS* 1.3 64.0 + - - +
32B PHE* 4.1 8.3 - - + -
59B SER* 3.7 32.8 - - - +
161B VAL 3.8 0.9 - - - +
162B SER* 3.3 3.1 - - - -
163B VAL* 2.8 51.4 + - + +
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Residues in contact with LYS 31 (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* 4.3 7.1 - - + +
30B VAL* 1.3 77.3 - - - +
32B PHE* 1.3 69.3 + - - +
160B GLU* 4.2 30.3 + - - +
161B VAL 3.3 11.2 - - - +
162B SER* 4.3 14.8 - - - -
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Residues in contact with PHE 32 (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* 4.1 8.5 - - + -
31B LYS* 1.3 81.5 - - - +
33B SER* 1.3 64.6 + - - +
57B PHE* 3.8 23.6 - + - -
58B SER 3.8 17.0 - - - +
59B SER* 3.6 35.4 - - - +
67B TRP* 3.4 37.5 - + - -
160B GLU* 3.4 4.2 - - - +
161B VAL* 2.8 66.0 + - + -
163B VAL* 4.3 15.0 - - + -
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Residues in contact with SER 33 (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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32B PHE* 1.3 85.0 - - - +
34B TYR* 1.3 64.9 + - - +
57B PHE* 4.7 5.7 - - - +
58B SER 5.1 2.8 - - - +
158B PHE* 3.5 29.3 - - - -
159B CYS 3.1 14.6 - - - -
160B GLU* 4.3 5.2 - - - -
161B VAL* 5.9 0.2 - - - -
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Residues in contact with TYR 34 (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* 1.3 76.9 - - - +
35B MET* 1.3 80.4 + - - +
36B TRP* 3.7 21.1 + + + -
54B SER* 4.1 13.5 - - - -
55B SER* 3.9 25.7 + - - -
56B THR 5.0 2.7 - - - -
57B PHE* 3.6 57.4 - + + -
69B LEU* 4.1 10.6 - - + +
157B LEU 4.0 0.5 - - - +
158B PHE* 3.6 7.3 - - - -
159B CYS* 2.9 33.9 + - + +
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Residues in contact with MET 35 (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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34B TYR* 1.3 89.3 + - - +
36B TRP* 1.3 59.2 + - - +
37B THR* 3.4 24.8 + - - +
107B LEU* 4.0 17.7 - - + -
156B THR* 3.4 28.7 - - + -
157B LEU 3.4 5.8 - - - +
158B PHE* 4.0 12.7 - - + -
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Residues in contact with TRP 36 (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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34B TYR* 3.7 20.5 + + + -
35B MET* 1.3 73.4 - - - +
37B THR* 1.3 72.8 + - - +
38B ILE* 3.7 24.0 + - + +
52B ILE* 3.5 32.1 - - + -
53B LYS 3.7 5.8 - - - -
54B SER* 3.5 38.2 - - - +
55B SER 5.1 0.4 - - - +
69B LEU* 3.7 38.1 - - + -
70B ARG 4.3 0.4 - - - -
71B VAL* 3.6 26.5 - - + -
86B LEU* 4.5 1.1 - - + -
155B LEU 3.5 1.9 - - - +
156B THR* 3.5 2.0 - - - -
157B LEU* 2.8 58.0 + - + +
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Residues in contact with THR 37 (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 27.6 + - - +
36B TRP* 1.3 81.6 + - - +
38B ILE* 1.3 63.5 + - - +
39B ASN* 3.8 29.0 + - - +
154B LYS* 4.1 16.6 - - + -
155B LEU 3.4 5.4 - - - +
156B THR* 3.8 18.4 + - - +
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Residues in contact with ILE 38 (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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36B TRP* 3.7 52.5 - - + +
37B THR* 1.3 71.6 - - - +
39B ASN* 1.3 70.1 + - - +
41B PHE* 3.8 25.8 - - + +
44B CYS* 4.8 3.1 - - - -
52B ILE* 4.8 15.9 - - + -
71B VAL* 4.0 14.6 - - + -
153B ASP 4.1 0.9 - - - +
154B LYS* 3.5 1.2 - - - -
155B LEU* 2.8 45.8 + - + +
157B LEU* 4.1 13.7 - - + -
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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