Contacts of the strand formed by residues 83 - 93 (chain B) in PDB entry 4JE4
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 TYR 83 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A THR* 3.6 23.8 - - + -
53A HIS 3.1 16.2 - - - +
54A ILE* 4.3 7.6 - - + -
89A LYS 4.6 2.7 - - - -
90A GLU* 3.2 31.3 - - + +
91A LYS* 2.9 40.5 + - + +
96A ILE* 5.2 2.0 - - + -
31B TYR* 2.8 17.9 + - - -
77B TYR* 2.8 57.6 + + + -
78B TYR 6.0 0.7 - - - -
81B PRO* 3.5 19.7 - - + -
82B THR* 1.3 74.9 - - - +
84B TYR* 1.3 65.3 + - - +
85B SER* 3.8 15.0 - - - -
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Residues in contact with TYR 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A ARG* 3.1 23.4 + - - -
36A SER* 4.8 3.2 + - - -
42A THR* 4.2 9.9 + - + +
53A HIS* 2.9 66.6 + + + +
55A LYS* 4.9 14.1 - - + -
31B TYR* 3.7 15.9 - + + +
33B VAL* 3.8 31.4 - - + -
48B GLU* 3.8 13.9 + - - -
74B TYR* 3.7 27.8 - + + -
75B ALA 3.2 15.5 - - - +
76B GLY* 3.6 9.2 - - - +
83B TYR* 1.3 77.8 - - - +
85B SER* 1.3 63.3 + - - +
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A VAL 3.8 19.5 - - - -
52A THR* 4.1 13.8 + - - +
90A GLU* 4.8 4.3 + - - -
3B SER* 5.4 0.9 + - - -
74B TYR* 3.5 12.2 - - - +
75B ALA 2.9 22.9 + - - +
77B TYR* 6.0 0.5 - - - -
83B TYR* 3.8 17.5 - - - -
84B TYR* 1.3 76.9 - - - +
86B SER* 1.3 80.8 + - - +
87B PRO* 3.3 3.9 - - - -
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Residues in contact with SER 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B SER* 3.0 40.2 + - - -
4B VAL* 3.7 20.1 - - - -
5B PRO* 3.3 16.5 - - - +
73B VAL 4.1 0.3 - - - +
75B ALA* 3.6 4.5 - - - +
77B TYR* 5.7 0.2 - - - -
85B SER* 1.3 85.4 + - - +
87B PRO* 1.3 74.1 - - - +
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Residues in contact with PRO 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A GLU* 5.3 3.4 - - - +
51A VAL 5.7 2.7 - - - +
4B VAL* 3.8 8.8 - - - +
72B THR* 3.5 24.2 - - + -
73B VAL 3.2 8.3 - - - +
74B TYR* 3.6 21.8 - - + -
85B SER* 3.3 4.9 - - - +
86B SER* 1.3 93.7 - - - +
88B ILE* 1.3 61.9 + - - +
89B SER* 5.1 2.0 - - - +
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Residues in contact with ILE 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B VAL* 4.4 4.5 - - + -
5B PRO* 3.2 41.1 - - + +
6B THR* 4.0 6.7 - - - -
7B LYS 4.1 2.2 - - - +
8B LEU* 3.6 40.5 - - + +
22B TRP* 5.8 0.2 - - + -
72B THR* 3.2 3.9 - - - -
73B VAL* 2.9 49.2 + - + +
87B PRO* 1.3 74.1 - - - +
89B SER* 1.3 71.4 + - - +
90B ILE* 5.4 2.2 - - + -
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Residues in contact with SER 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.4 0.2 - - - -
70B THR* 4.5 10.6 - - - +
71B ILE 3.2 4.0 - - - -
72B THR* 2.8 31.2 + - - +
87B PRO* 5.1 2.1 - - - +
88B ILE* 1.3 79.2 - - - +
90B ILE* 1.3 71.3 + - - +
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Residues in contact with ILE 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 3.3 54.5 - - + +
9B GLU* 4.3 0.9 - - - -
10B VAL* 4.0 33.9 - - + +
20B ILE* 5.0 1.1 - - + -
70B THR* 3.4 6.3 - - - +
71B ILE* 3.0 43.8 + - + +
88B ILE* 5.4 2.2 - - + -
89B SER* 1.3 81.4 - - - +
91B ASN* 1.3 76.0 + - - +
92B TYR* 6.0 0.2 - - + -
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Residues in contact with ASN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B THR* 3.2 15.1 + - - +
68B ASP* 6.2 2.5 - - + -
69B TYR 3.2 4.9 - - - +
70B THR* 2.8 29.2 + - - +
71B ILE* 5.4 0.2 - - - -
90B ILE* 1.3 84.8 - - - +
92B TYR* 1.3 68.8 + - - +
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Residues in contact with TYR 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 3.8 37.6 - - + +
13B ALA* 3.2 23.2 - - + +
18B LEU* 3.5 37.2 - - + -
67B VAL 3.6 1.2 - - - +
68B ASP* 4.5 1.6 - - - -
69B TYR* 2.8 40.8 + - - +
71B ILE* 4.4 5.4 - - + -
90B ILE* 5.4 0.4 - - + -
91B ASN* 1.3 78.4 - - - +
93B ARG* 1.3 81.2 + - - +
94B THR* 3.8 6.1 + - - +
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Residues in contact with ARG 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66B GLY* 3.4 31.1 + - - -
67B VAL* 3.3 13.9 - - - +
68B ASP* 3.1 31.5 + - - +
92B TYR* 1.3 86.4 - - - +
94B THR* 1.3 71.7 + - - +
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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