Contacts of the strand formed by residues 36 - 43 (chain A) in PDB entry 5H8Q
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 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A CYS* 4.1 4.9 - - - -
35A THR* 1.3 77.4 - - - +
37A PRO* 1.3 74.8 - - + +
57A CYS* 3.5 1.6 - - - -
58A CYS* 2.8 33.5 + - + +
63A ILE* 3.6 22.0 - - + -
66A LEU* 5.3 0.4 - - + -
67A LYS* 3.8 27.6 - - + -
77A TYR* 3.4 27.6 - - + +
79A LEU* 3.7 25.8 - - + -
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Residues in contact with PRO 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ILE* 5.8 1.8 - - + -
31A CYS* 3.6 24.8 - - + -
35A THR 4.9 0.2 - - - +
36A VAL* 1.3 91.1 - - + +
38A CYS* 1.3 60.2 + - - +
55A LYS* 6.5 1.6 - - + -
56A LYS 4.4 0.9 - - - +
77A TYR* 5.1 3.9 - - + -
79A LEU* 3.7 18.1 + - - +
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Residues in contact with CYS 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A THR* 5.2 0.2 - - + -
21A VAL* 4.7 0.2 - - - -
37A PRO* 1.3 76.0 - - - +
39A ARG* 1.3 62.3 + - - +
55A LYS* 5.0 0.7 - - - -
56A LYS* 2.8 41.2 + - - +
57A CYS 3.5 6.5 - - - -
58A CYS* 2.0 57.2 - - - -
79A LEU* 3.3 25.1 - - + +
80A TYR 4.9 0.4 - - - +
81A LEU* 4.4 9.4 - - + -
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Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A SER* 4.9 2.2 + - - -
38A CYS* 1.3 75.1 - - - +
40A LYS* 1.3 62.0 + - - +
41A PHE 5.8 0.2 - - - +
53A ASN* 3.9 38.3 + - + +
54A VAL 3.2 13.9 - - - +
55A LYS* 4.8 6.3 - - + -
78A ASP* 2.9 41.8 + - - +
79A LEU 3.1 10.3 + - - +
80A TYR* 3.3 21.5 - - + +
81A LEU* 2.8 28.9 + - - +
301A ACT 2.8 41.0 + - - -
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Residues in contact with LYS 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A VAL* 6.2 0.8 - - - +
39A ARG* 1.3 77.2 - - - +
41A PHE* 1.3 70.1 + - - +
42A VAL* 3.5 19.6 + - + +
52A MET 3.4 0.7 - - - +
53A ASN* 4.2 2.9 - - - -
54A VAL* 2.8 40.3 + - + +
56A LYS* 4.7 19.9 - - + +
81A LEU* 3.9 33.0 - - + -
82A VAL 5.7 0.7 - - - +
83A THR* 4.1 13.5 - - + -
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Residues in contact with PHE 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A ARG* 5.8 0.4 - - - +
40A LYS* 1.3 72.8 - - - +
42A VAL* 1.3 62.6 + - - +
43A LYS* 3.8 33.0 - - + -
49A ASN 3.8 11.2 - - - -
51A GLY* 3.5 40.2 - - - -
52A MET 3.5 7.4 - - - -
53A ASN* 3.8 23.3 + - - +
81A LEU 5.0 1.2 + - - +
83A THR* 3.4 37.4 - - + +
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Residues in contact with VAL 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LYS* 3.6 34.8 - - - +
41A PHE* 1.3 78.2 - - - +
43A LYS* 1.3 72.4 + - - +
44A ILE* 4.6 1.4 - - - +
51A GLY* 3.1 1.5 - - - -
52A MET* 2.8 41.2 + - + +
54A VAL* 3.7 20.4 - - + -
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Residues in contact with LYS 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 3.8 21.6 + - + -
42A VAL* 1.3 85.9 - - - +
44A ILE* 1.3 65.1 + - - +
45A ASN* 3.8 14.5 - - - +
46A ASN* 5.3 4.9 - - - +
48A THR 4.0 11.7 - - - +
49A ASN* 3.2 37.4 + - - +
50A GLU 3.6 13.7 - - - +
51A GLY* 4.0 0.4 - - - -
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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