Contacts of the strand formed by residues 74 - 85 (chain A) in PDB entry 3HMX
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 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A THR* 3.7 24.0 - - + -
69A HIS* 3.8 25.1 - - + +
72A GLY 3.8 1.1 + - - +
73A GLU* 1.3 77.5 - - - +
75A LEU* 1.3 68.7 + - - +
76A SER* 4.0 10.3 - - - +
77A HIS* 6.0 0.9 - - + +
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Residues in contact with LEU 75 (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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28A CYS* 3.5 22.7 - - - -
29A ASP 5.0 3.3 - - - +
30A THR* 3.5 28.3 - - + +
32A GLU* 5.4 3.4 - - - +
36A ILE* 4.3 18.6 - - + -
68A CYS* 2.9 23.1 + - - +
69A HIS* 4.3 3.4 - - - +
70A LYS* 4.0 28.3 - - + +
73A GLU 3.8 2.0 + - - +
74A VAL* 1.3 82.9 - - - +
76A SER* 1.3 63.5 + - - +
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Residues in contact with SER 76 (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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7A ASP* 5.2 3.3 + - - -
27A THR 5.2 0.5 + - - -
28A CYS* 4.4 1.3 - - - -
29A ASP* 3.5 42.0 + - - +
67A THR* 3.2 23.5 - - - +
68A CYS* 3.3 18.5 + - - -
74A VAL* 4.6 4.3 - - - -
75A LEU* 1.3 82.1 - - - +
77A HIS* 1.3 71.4 + - - +
78A SER* 5.4 0.3 + - - -
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Residues in contact with HIS 77 (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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7A ASP* 3.1 52.1 + - + +
8A VAL* 5.7 2.0 - - - +
38A TRP* 6.1 1.3 - - - -
65A GLN* 4.2 14.6 - - + +
66A TYR 3.2 12.3 - - - +
67A THR* 4.0 12.1 - - + +
68A CYS 5.0 0.2 - - - +
74A VAL* 6.0 0.8 - - + +
76A SER* 1.3 85.2 + - - +
78A SER* 1.3 67.3 + - - +
79A LEU* 4.1 10.3 - - + +
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Residues in contact with SER 78 (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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7A ASP* 3.9 5.3 + - - -
9A TYR* 3.8 25.3 + - - -
26A LEU* 4.5 14.9 - - - +
27A THR 4.4 12.6 + - - -
38A TRP* 4.8 6.5 - - - -
64A GLY 3.5 1.4 - - - +
65A GLN* 3.4 1.7 - - - -
66A TYR* 2.8 45.6 + - - +
76A SER* 5.4 0.7 + - - -
77A HIS* 1.3 78.8 + - - +
79A LEU* 1.3 62.0 + - - +
80A LEU* 4.1 6.7 - - - +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A ASP 3.2 14.8 + - - +
8A VAL* 4.3 20.6 - - + -
9A TYR* 3.1 22.2 + - - -
64A GLY* 3.5 29.6 - - - -
65A GLN* 3.8 13.7 - - + +
77A HIS* 4.1 7.6 - - + +
78A SER* 1.3 74.0 - - - +
80A LEU* 1.3 76.2 + - - +
81A LEU* 4.1 18.8 - - + -
195A LYS 6.0 0.2 - - - +
196A LEU* 4.4 8.3 - - + -
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Residues in contact with LEU 80 (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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1A ILE* 5.1 1.6 - - + -
9A TYR* 3.3 27.8 - - + +
11A VAL* 4.4 15.0 - - + -
24A VAL* 4.9 4.3 - - + -
26A LEU* 4.4 18.4 - - + -
55A ILE* 4.6 4.5 - - + -
57A VAL* 4.3 26.2 - - + -
62A ASP 4.7 2.0 - - - +
63A ALA* 3.5 11.4 - - + +
64A GLY 3.1 30.2 + - - +
66A TYR* 4.2 24.5 - - + -
78A SER* 4.1 6.5 - - - +
79A LEU* 1.3 96.8 - - - +
81A LEU* 1.3 72.3 + - - +
82A LEU* 5.5 1.3 - - + -
196A LEU* 3.9 2.1 - - - +
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Residues in contact with LEU 81 (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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4A LEU* 4.1 11.7 - - + -
8A VAL* 4.0 24.7 - - + -
9A TYR 2.9 7.8 + - - +
10A VAL* 3.4 7.7 - - + -
11A VAL* 3.0 25.8 + - - +
79A LEU* 4.1 20.6 - - + -
80A LEU* 1.3 82.2 - - - +
82A LEU* 1.3 67.4 + - - +
193A VAL* 3.8 32.5 - - + -
195A LYS 3.9 17.5 - - - +
196A LEU* 3.3 19.1 - - - +
198A TYR* 3.8 13.7 - - + -
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Residues in contact with LEU 82 (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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11A VAL* 3.4 29.2 - - + +
13A LEU* 4.5 22.4 - - + -
57A VAL* 3.8 13.7 - - + -
59A GLU* 3.8 10.8 - - - +
60A PHE* 3.4 57.1 - - + +
63A ALA* 4.2 12.8 - - + -
80A LEU* 5.3 2.0 - - + -
81A LEU* 1.3 77.7 - - - +
83A HIS* 1.3 61.6 + - - +
84A LYS* 3.9 6.3 + - - +
196A LEU 3.0 7.7 + - - -
197A LYS* 3.8 6.6 - - - +
198A TYR* 3.0 25.3 + - - +
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Residues in contact with HIS 83 (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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10A VAL* 3.8 18.8 - - + +
11A VAL 3.0 8.5 + - - +
12A GLU* 3.2 6.1 - - + -
13A LEU* 3.1 25.9 + - - +
81A LEU 4.1 0.8 + - - -
82A LEU* 1.3 72.5 - - - +
84A LYS* 1.3 62.6 + - - +
90A TRP* 3.6 43.1 - + + -
91A SER* 4.4 3.5 + - - -
198A TYR* 3.0 25.5 + + + -
199A GLU* 3.6 28.0 - - + -
200A ASN* 4.1 7.6 + - - -
1C NAG 2.8 39.3 + - - -
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Residues in contact with LYS 84 (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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13A LEU* 3.8 17.7 - - - +
15A TRP* 2.9 64.2 - - + +
60A PHE* 3.5 37.6 - - + +
82A LEU* 3.9 8.2 + - - +
83A HIS* 1.3 74.7 + - - +
85A LYS* 1.3 63.8 + - - +
86A GLU* 3.8 6.4 + - + +
90A TRP* 3.5 4.7 - - - -
91A SER* 2.9 47.8 + - - +
197A LYS* 5.6 4.9 - - + -
198A TYR 4.7 0.2 + - - -
57H ASP* 4.8 2.8 + - - -
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Residues in contact with LYS 85 (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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13A LEU 3.2 14.5 + - - +
14A ASP* 3.1 45.8 - - + +
15A TRP 3.2 2.3 + - - -
83A HIS 3.8 0.4 + - - -
84A LYS* 1.3 70.8 - - - +
86A GLU* 1.3 65.3 + - - +
88A GLY* 3.0 35.2 + - - +
89A ILE 3.4 12.3 - - - +
90A TRP* 3.7 42.9 - - + +
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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