Contacts of the strand formed by residues 54 - 63 (chain A) in PDB entry 1HIB
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 ASP 54 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A SER* 5.2 0.5 - - - -
53A ASN* 1.3 82.0 + - + +
55A LYS* 1.3 71.8 + - - +
56A ILE* 4.7 6.3 - - - +
103A LYS 3.2 4.9 - - - +
104A ILE* 3.4 12.0 - - - +
105A GLU* 2.9 56.9 + - + +
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Residues in contact with LYS 55 (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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50A GLU* 4.3 7.6 - - - +
51A GLU* 3.3 6.9 - - - -
52A SER* 3.2 55.9 + - - +
54A ASP* 1.3 85.0 - - - +
56A ILE* 1.3 67.2 + - - +
57A PRO* 4.3 0.4 - - - -
102A ASN* 3.7 32.2 - - + +
103A LYS 3.4 2.5 - - - -
104A ILE* 3.7 25.8 - - + +
113A GLU* 4.0 17.2 + - - -
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Residues in contact with ILE 56 (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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46A PHE* 3.6 27.1 - - + -
47A VAL 5.7 0.7 - - - +
51A GLU* 4.7 10.5 - - + -
52A SER 5.0 2.5 - - - +
53A ASN 5.5 2.0 - - - +
54A ASP* 4.7 4.7 - - - +
55A LYS* 1.3 86.7 - - - +
57A PRO* 1.3 80.0 - - + +
58A VAL* 3.5 0.8 + - + +
102A ASN* 4.4 2.0 - - - -
103A LYS* 2.8 60.7 + - - +
105A GLU* 5.8 4.7 - - + +
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Residues in contact with PRO 57 (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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46A PHE* 3.8 0.7 - - - -
47A VAL* 3.2 28.7 + - + +
48A GLN 4.0 10.3 - - - +
49A GLY* 3.5 34.3 - - - +
50A GLU 3.5 10.8 - - - +
51A GLU* 3.5 21.5 - - + -
56A ILE* 1.3 90.9 - - + +
58A VAL* 1.3 64.8 + - - +
100A VAL* 3.9 19.5 - - + -
101A PHE 3.4 7.4 - - - +
102A ASN* 4.1 7.9 - - - +
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Residues in contact with VAL 58 (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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44A MET* 3.9 22.2 - - + -
45A SER 3.1 13.2 - - - +
46A PHE* 4.0 18.8 - - + -
47A VAL* 3.8 5.6 - - - -
56A ILE* 3.7 9.0 - - + +
57A PRO* 1.3 81.4 - - - +
59A ALA* 1.3 62.8 - - - +
60A LEU* 4.5 7.0 - - + -
100A VAL* 3.5 5.5 - - - +
101A PHE* 2.8 43.4 + - + +
103A LYS* 4.1 13.0 - - + -
112A PHE* 4.0 29.4 - - + -
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Residues in contact with ALA 59 (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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43A SER 3.6 1.7 - - - +
44A MET* 3.3 6.8 - - - +
45A SER* 3.0 32.6 + - - -
47A VAL* 3.9 20.6 - - + -
58A VAL* 1.3 75.3 - - - +
60A LEU* 1.3 63.2 + - - +
61A GLY 4.0 0.4 - - - -
68A TYR* 4.1 20.6 - - + -
95A MET* 4.4 13.5 - - + -
99A PHE 3.8 13.5 - - - +
101A PHE* 5.2 0.2 - - - -
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Residues in contact with LEU 60 (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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8A CYS* 5.8 0.4 - - - -
10A LEU* 4.6 15.0 - - + -
42A PHE* 4.4 19.7 - - + -
43A SER 3.8 0.9 - - - -
44A MET* 3.9 36.8 - - + -
58A VAL* 4.5 3.8 - - + -
59A ALA* 1.3 72.7 - - - +
61A GLY* 1.3 59.7 - - - +
68A TYR* 3.5 6.9 - - - -
69A LEU* 2.9 48.5 + - + +
99A PHE 4.5 4.6 + - - -
101A PHE* 3.9 17.1 - - + -
112A PHE* 4.0 18.6 - - + -
122A ILE* 3.9 28.3 - - + -
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Residues in contact with GLY 61 (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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42A PHE* 3.1 8.4 - - - +
43A SER* 2.7 43.4 + - - -
60A LEU* 1.3 74.2 - - - +
62A LEU* 1.3 64.9 + - - -
67A LEU 3.4 9.9 - - - -
68A TYR* 3.7 21.0 - - - -
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Residues in contact with LEU 62 (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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20A MET* 3.5 30.1 - - + -
26A LEU* 4.9 2.5 - - + -
40A VAL* 4.1 15.3 - - + -
41A VAL 3.9 4.0 - - - -
42A PHE* 4.4 8.1 - - + +
43A SER* 5.2 0.4 - - - -
61A GLY* 1.3 71.0 - - - -
63A LYS* 1.3 69.6 - - - +
64A GLU 3.1 0.9 + - - -
65A LYS* 3.0 30.4 + - + +
66A ASN* 3.8 5.0 + - - -
67A LEU* 2.9 33.8 + - + +
68A TYR* 6.0 0.5 - - - -
69A LEU* 3.8 30.1 - - + -
82A LEU* 3.8 23.6 - - + -
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Residues in contact with LYS 63 (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 ASN* 3.8 32.1 - - - +
41A VAL* 2.9 48.6 + - + +
43A SER* 4.5 13.2 - - - -
61A GLY 3.4 3.8 + - - -
62A LEU* 1.3 71.2 - - - +
64A GLU* 1.3 96.0 + - + +
65A LYS* 3.4 6.4 + - - +
151A VAL* 6.0 1.6 - - - +
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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