Contacts of the strand formed by residues 82 - 94 (chain A) in PDB entry 4OBZ
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 SER 82 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ILE 2.9 9.7 + - - -
77A HIS* 2.8 25.8 + - - -
81A GLY* 1.3 74.4 - - - -
83A LEU* 1.3 64.8 + - - +
121B GLN* 3.9 2.9 - - - -
122B PRO* 3.2 33.9 + - - +
126B PHE* 4.0 6.8 - - - -
174D ASP* 2.7 39.8 + - - -
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Residues in contact with LEU 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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40A TRP* 3.4 51.6 - - + +
74A PHE* 3.6 22.0 - - + -
75A ASP* 3.5 3.9 - - - +
76A ILE* 2.8 42.1 + - + +
78A TYR* 3.6 23.1 - - + -
82A SER* 1.3 77.0 - - - +
84A SER* 1.3 62.1 + - - +
118B ALA* 3.6 21.3 - - + -
120B LYS 3.3 13.5 - - - +
121B GLN* 4.2 9.6 - - + -
122B PRO* 4.4 2.2 - - - -
126B PHE* 4.3 4.3 - - + -
174D ASP* 4.9 1.6 - - - -
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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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74A PHE* 3.2 22.2 - - - -
75A ASP* 3.7 17.3 - - - -
83A LEU* 1.3 76.4 - - - +
85A GLY* 1.3 60.0 + - - +
118B ALA* 3.6 4.7 - - - -
119B THR* 3.1 18.3 + - - -
120B LYS* 3.1 36.1 + - - +
174D ASP* 5.3 2.0 + - - -
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Residues in contact with GLY 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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73A SER* 3.4 8.8 - - - -
74A PHE* 2.9 33.5 + - - +
84A SER* 1.3 76.7 - - - +
86A TYR* 1.3 61.4 + - - +
117B GLU 3.4 13.0 - - - -
119B THR* 3.6 15.3 - - - -
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Residues in contact with TYR 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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43A SER* 4.0 5.2 - - - -
45A HIS* 3.4 26.4 + + + -
61A SER* 4.8 2.9 + - - -
67A TYR* 4.6 8.4 + - - -
71A GLY* 3.6 25.8 - - - +
72A THR 3.3 5.6 - - - +
73A SER* 4.6 2.7 - - - +
74A PHE* 3.5 6.8 - - - -
85A GLY* 1.3 73.3 - - - +
87A LEU* 1.3 70.0 + - - +
88A SER* 3.7 5.2 - - - -
117B GLU* 2.8 69.2 + - + +
119B THR* 3.8 28.0 - - + -
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Residues in contact with LEU 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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38A ASN* 6.0 2.5 - - - +
70A ASN* 3.5 25.6 - - - +
71A GLY 3.0 24.1 + - - -
72A THR* 2.7 32.7 + - + +
74A PHE* 4.1 21.8 - - + -
86A TYR* 1.3 75.8 - - - +
88A SER* 1.3 66.6 + - - +
400A NAG 4.1 15.5 - - - +
114B VAL* 4.2 14.6 - - + -
115B PHE 3.5 18.2 - - - +
116B GLY* 4.3 4.0 - - - +
144B VAL 5.6 1.3 - - - +
145B ASN* 4.6 9.9 - - + -
147B VAL* 4.2 19.5 - - + -
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Residues in contact with SER 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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67A TYR* 3.1 26.5 + - - -
68A VAL 4.0 4.0 - - - -
70A ASN* 4.2 5.2 - - - -
86A TYR* 3.7 2.6 + - - -
87A LEU* 1.3 77.0 + - - +
89A GLN* 1.3 58.6 + - - +
114B VAL* 3.3 6.1 - - - +
115B PHE* 2.8 51.1 + - - +
117B GLU* 2.7 30.5 + - - -
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Residues in contact with GLN 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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66A THR 4.7 0.4 - - - -
67A TYR* 3.5 3.8 - - - -
68A VAL* 2.8 72.4 + - + +
69A LYS 6.0 0.2 - - - -
70A ASN* 5.8 2.5 - - + -
88A SER* 1.3 74.1 - - - +
90A ASP* 1.3 65.6 + - - +
112B ARG* 3.3 53.9 + - - +
113B GLN 3.2 9.2 - - - +
114B VAL* 4.0 17.3 - - + +
115B PHE* 4.1 1.1 - - - -
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Residues in contact with ASP 90 (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 ILE* 3.8 16.4 - - + -
22A GLY* 3.2 14.1 - - - -
59A TYR* 2.6 25.5 + - - +
64A SER* 2.7 16.3 + - - -
66A THR* 2.7 38.6 + - - -
67A TYR* 3.7 7.4 - - - -
89A GLN* 1.3 74.8 - - - +
91A THR* 1.4 67.1 + - - +
92A VAL* 4.2 2.5 - - - +
112B ARG* 4.6 3.4 - - - +
113B GLN* 3.0 34.9 + - - +
115B PHE* 3.8 7.0 - - + -
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Residues in contact with THR 91 (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 GLY 3.6 0.7 - - - +
21A ILE* 3.4 5.5 - - - +
22A GLY 2.9 29.2 + - - +
23A THR* 4.3 8.1 - - - +
66A THR* 3.6 27.7 + - - +
90A ASP* 1.4 79.1 + - - +
92A VAL* 1.4 63.4 + - - +
93A SER* 4.0 2.8 + - - +
109B LYS* 4.0 35.4 - - + -
110B VAL 3.4 12.1 - - - +
111B GLU* 4.2 16.7 - - + +
112B ARG 4.6 1.7 + - - -
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Residues in contact with VAL 92 (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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19A ILE* 4.1 19.7 - - + -
20A GLY 3.3 7.9 - - - +
21A ILE* 4.5 10.3 - - + -
39A LEU* 3.7 18.2 - - + -
90A ASP 4.2 2.5 - - - +
91A THR* 1.4 75.2 - - - +
93A SER* 1.3 65.4 + - - +
94A VAL* 4.4 11.0 - - + +
108B VAL 3.8 1.0 - - - +
109B LYS* 3.6 1.4 - - - -
110B VAL* 2.7 49.9 + - + +
113B GLN* 3.7 32.1 - - + +
115B PHE* 5.5 1.1 - - + -
135B LEU* 4.7 6.7 - - + -
150B VAL* 4.8 6.7 - - + -
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Residues in contact with SER 93 (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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19A ILE* 3.5 2.9 - - - +
20A GLY* 2.8 35.9 + - - -
22A GLY 4.6 4.3 + - - -
25A PRO* 3.6 18.9 - - - +
91A THR* 4.6 1.7 + - - +
92A VAL* 1.3 70.8 - - - +
94A VAL* 1.3 68.4 + - - +
95A PRO 3.1 6.2 - - - +
96A CYS 3.5 20.4 - - - -
97A GLN* 3.6 10.5 - - - -
108B VAL 3.4 5.2 - - - -
109B LYS* 3.7 19.2 - - - +
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Residues in contact with VAL 94 (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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3A ILE* 3.6 7.9 - - + +
5A GLU* 3.5 32.5 - - + +
19A ILE* 3.8 18.6 - - + -
32A PHE* 4.6 7.9 - - + -
92A VAL* 4.4 12.8 - - + +
93A SER* 1.3 79.5 - - - +
95A PRO* 1.4 62.0 + - - +
97A GLN* 3.7 1.3 - - - -
107B GLY* 3.4 1.4 - - - -
108B VAL* 3.0 40.4 + - + +
110B VAL* 5.8 1.8 - - + -
135B LEU* 4.9 3.8 - - + -
150B VAL* 5.5 5.8 - - + -
154B LEU* 6.3 0.4 - - + -
181B LEU* 5.5 0.2 - - + -
183B LEU* 3.8 24.2 - - + -
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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