Contacts of the strand formed by residues 83 - 89 (chain A) in PDB entry 1NB9
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 LYS 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A GLU* 6.2 0.2 - - - +
42A VAL* 3.6 26.9 - - + +
43A ASP* 5.1 3.6 + - - +
45A LEU* 4.9 9.2 - - + -
46A PRO 5.4 0.8 + - - -
47A ALA* 4.4 18.0 + - - +
49A ILE 3.8 19.9 + - - +
50A SER* 4.6 2.0 - - - +
51A THR* 4.1 13.7 - - + +
72A ILE* 4.0 16.6 - - + -
73A GLY 3.2 13.5 - - - +
74A TRP* 3.8 37.4 - - + -
75A ASN* 4.0 10.2 + - - +
78A TYR* 5.7 0.9 - - - -
81A THR 5.1 0.2 - - - +
82A LYS* 1.3 81.0 - - - +
84A SER* 1.3 62.9 + - - +
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Residues in contact with SER 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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42A VAL* 4.1 5.2 - - - -
71A SER 4.3 1.0 + - - -
72A ILE* 3.3 9.2 - - - +
73A GLY* 2.8 45.1 + - - +
74A TRP 4.2 4.0 + - - -
75A ASN* 4.5 15.7 - - - -
83A LYS* 1.3 74.9 - - - +
85A MET* 1.3 64.0 + - - +
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Residues in contact with MET 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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15A CYS* 4.1 13.0 - - - -
35A ALA 4.2 0.2 - - - +
36A ASN* 4.0 18.2 - - - +
37A PHE* 3.4 46.2 + - + +
41A VAL* 4.8 4.0 - - - -
42A VAL* 3.9 26.4 - - + +
45A LEU* 4.7 17.9 - - + -
70A VAL* 3.8 19.3 - - + -
71A SER 3.4 5.2 - - - -
72A ILE* 4.5 6.1 - - + -
84A SER* 1.3 77.5 - - - +
86A GLU* 1.3 67.3 + - - +
87A THR* 4.2 8.1 - - - +
104A VAL* 4.3 4.7 - - + -
106A ILE* 4.1 21.8 - - + -
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Residues in contact with GLU 86 (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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34A THR* 3.2 21.7 + - + -
35A ALA 3.3 7.9 - - - +
36A ASN* 3.8 16.1 - - - +
69A VAL 4.1 0.2 - - - +
70A VAL* 3.2 3.8 - - - -
71A SER* 2.9 43.8 + - - +
85A MET* 1.3 76.4 - - - +
87A THR* 1.3 63.9 + - - +
201A MG 4.0 1.9 - - - -
401A RBF 2.6 67.4 + - + +
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Residues in contact with THR 87 (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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34A THR* 3.4 3.2 - - - -
35A ALA* 2.8 38.4 + - - +
37A PHE* 4.9 1.7 - - - -
68A MET* 4.0 22.4 - - + -
69A VAL 3.4 10.1 - - - +
70A VAL* 3.3 20.9 - - + +
85A MET* 4.2 12.1 - - - +
86A GLU* 1.3 76.0 - - - +
88A HIS* 1.3 60.8 + - - +
89A ILE* 4.3 11.7 - - + -
102A LEU* 4.1 15.7 - - + +
104A VAL* 4.3 14.4 - - + +
301A ADP 3.5 7.4 - - - -
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Residues in contact with HIS 88 (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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31A GLY 4.7 2.9 - - - -
32A ILE* 3.6 20.3 - - + +
33A PRO* 2.8 44.9 + - + +
34A THR* 4.5 7.1 - - + +
68A MET* 3.3 3.0 - - - -
69A VAL* 2.9 41.8 + - + -
86A GLU 4.2 0.6 + - - -
87A THR* 1.3 72.2 - - - +
89A ILE* 1.3 82.0 + - - +
90A MET* 4.0 13.0 + - - +
130A ILE* 3.6 29.9 - - + +
301A ADP 3.9 4.2 + - - -
401A RBF 4.5 3.5 - - + +
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Residues in contact with ILE 89 (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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35A ALA* 6.0 0.2 - - + -
58A ALA* 4.0 20.4 - - + +
59A SER 5.4 0.2 - - - -
60A VAL* 4.0 9.2 - - + -
66A HIS* 3.6 30.5 - - + -
67A LYS 3.6 6.3 - - - +
68A MET* 4.0 1.1 - - + -
87A THR* 4.3 9.4 - - + -
88A HIS* 1.3 84.7 + - - +
90A MET* 1.3 61.0 + - - +
91A HIS* 2.9 15.4 + - + +
93A PHE* 3.9 22.2 - - + -
97A PHE* 4.0 11.4 - - + -
102A LEU* 3.9 26.0 - - + -
301A ADP 2.7 39.7 + - + +
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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