Contacts of the strand formed by residues 96 - 108 (chain R) in PDB entry 4N3E
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 ILE 96 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92R LEU* 3.4 32.3 + - + +
93R ARG 4.4 2.3 - - - +
94R ASP 3.2 3.1 + - - +
95R ASN* 1.3 92.7 - - - +
97R GLU* 1.3 63.6 + - - +
98R LYS* 3.7 19.3 - - - +
99R VAL* 4.2 12.1 - - + -
120R TYR* 4.1 14.1 - - + -
121R HIS 3.4 17.9 - - - +
122R PRO* 4.2 0.2 - - - -
123R LYS* 3.9 15.4 - - - +
128R VAL* 4.3 18.4 - - + -
132R GLU* 3.1 36.8 - - + +
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Residues in contact with GLU 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87R PHE 4.2 6.4 - - - +
92R LEU* 3.8 17.8 - - - +
96R ILE* 1.3 73.8 - - - +
98R LYS* 1.3 84.4 + - + +
121R HIS* 2.5 24.6 + - + +
122R PRO 4.0 10.9 - - - +
123R LYS* 3.7 26.7 - - + +
124R PRO* 4.8 9.5 - - + +
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Residues in contact with LYS 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85R THR* 3.8 19.1 + - + +
86R LEU 3.2 17.9 - - - +
87R PHE* 4.5 5.8 - - + -
92R LEU* 4.8 2.7 - - - -
96R ILE* 3.6 4.5 - - - +
97R GLU* 1.3 100.2 - - + +
99R VAL* 1.3 65.9 + - - +
100R VAL* 4.4 9.9 - - - +
121R HIS* 2.9 62.7 + - + +
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Residues in contact with VAL 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85R THR* 3.4 2.5 - - - +
86R LEU* 2.8 50.6 + - + +
92R LEU* 4.7 4.9 - - + -
96R ILE* 4.2 7.9 - - + -
98R LYS* 1.3 80.0 - - - +
100R VAL* 1.3 62.9 - - - +
101R TYR* 3.7 31.4 - - + +
118R VAL* 3.9 18.4 - - + -
119R THR 3.5 7.0 - - - +
120R TYR* 3.9 32.3 - - + -
202R 2AN 5.0 4.0 - - + -
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Residues in contact with VAL 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83R LYS* 4.7 21.8 - - + -
84R TYR 3.5 6.5 - - - +
85R THR* 3.2 28.3 - - + +
98R LYS* 4.4 9.4 - - - +
99R VAL* 1.3 72.2 - - - +
101R TYR* 1.4 67.5 + - - +
102R GLU* 4.8 1.8 - - + +
117R THR 3.7 2.3 - - - +
118R VAL* 3.5 3.8 - - - -
119R THR* 2.9 47.3 + - - +
121R HIS* 3.8 25.1 - - + +
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Residues in contact with TYR 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27R ARG* 5.9 1.1 - - - -
70R HIS* 4.1 18.6 - - - -
83R LYS* 3.3 3.6 - - - +
84R TYR* 2.6 85.7 + + + +
86R LEU* 4.2 4.9 - - + +
99R VAL* 3.7 33.4 - - + +
100R VAL* 1.4 72.6 - - - +
102R GLU* 1.3 57.4 + - - +
103R VAL* 4.2 4.3 - - + -
116R ILE* 5.6 1.3 - - + -
117R THR 3.9 4.0 - - - -
118R VAL* 3.9 28.3 - - + -
120R TYR* 4.8 1.2 + - - -
136R GLY 4.9 8.1 + - - -
140R ALA* 5.3 7.9 - - + -
201R 2AN 4.8 9.0 - + - -
202R 2AN 3.3 44.0 + - - -
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Residues in contact with GLU 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115Q LYS* 5.8 0.5 + - - -
81R TYR* 3.8 27.1 + - + -
82R CYS 3.3 4.3 - - - +
83R LYS* 3.7 28.4 - - + +
100R VAL* 4.1 3.0 + - + +
101R TYR* 1.3 71.1 - - - +
103R VAL* 1.3 63.3 + - - +
115R LYS* 2.3 37.0 + - - +
116R ILE* 3.4 7.4 - - - +
117R THR* 3.1 46.0 + - - +
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Residues in contact with VAL 103 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R PHE* 4.6 5.6 - - + -
24R VAL* 4.3 8.7 - - + -
81R TYR* 3.2 6.7 - - - -
82R CYS* 2.7 40.2 + - + +
84R TYR* 4.2 14.6 - - + -
101R TYR* 4.9 1.1 - - + -
102R GLU* 1.3 81.2 - - - +
104R LYS* 1.3 66.5 + - - +
105R LEU* 3.7 24.9 - - + -
115R LYS 3.7 6.1 - - - -
116R ILE* 4.2 9.6 - - + -
201R 2AN 3.5 46.2 - - + -
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Residues in contact with LYS 104 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79R ASN* 3.1 32.9 + - - +
80R PHE 3.0 6.7 - - - +
81R TYR* 3.7 27.8 - - + -
103R VAL* 1.3 79.0 - - - +
105R LEU* 1.3 69.6 + - - +
106R GLU* 5.3 5.6 + - + +
113R LYS 4.1 0.3 - - - +
114R GLY* 3.5 1.9 - - - -
115R LYS* 3.3 51.4 + - + +
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Residues in contact with LEU 105 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16R PRO* 3.7 29.6 - - + +
19R LEU* 3.8 26.0 - - + -
20R PHE* 3.9 10.3 - - + +
79R ASN 3.6 16.8 - - - +
80R PHE* 2.7 30.3 + - + +
103R VAL* 3.7 20.4 - - + -
104R LYS* 1.3 89.1 + - - +
106R GLU* 1.3 67.4 + - - +
112R SER* 4.7 3.8 - - - +
113R LYS 3.5 5.8 - - - +
114R GLY* 3.9 15.0 - - - -
116R ILE* 5.3 1.3 - - + -
201R 2AN 3.9 22.7 - - + -
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Residues in contact with GLU 106 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J ASN* 5.2 5.6 - - - +
16R PRO* 4.1 4.7 - - - -
80R PHE* 4.3 4.7 - - - -
104R LYS* 5.3 5.8 + - + +
105R LEU* 1.3 81.2 - - - +
107R ALA* 1.3 74.9 + - - +
108R VAL* 4.9 1.4 - - - +
112R SER* 3.3 4.2 - - - -
113R LYS* 3.0 66.3 + - + +
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Residues in contact with ALA 107 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16J PRO* 5.0 0.9 - - + -
78J ALA 4.1 5.1 - - - +
79J ASN* 5.0 4.5 - - - +
80J PHE* 3.8 30.1 - - + -
107J ALA* 4.2 12.8 - - + +
16R PRO* 3.7 22.8 - - + +
80R PHE* 4.8 2.2 - - - -
106R GLU* 1.3 83.6 - - - +
108R VAL* 1.3 69.7 + - - +
109R GLY 4.0 0.9 - - - +
111R GLY 3.5 6.3 - - - +
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Residues in contact with VAL 108 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J ALA* 3.5 17.7 - - + -
11R GLU* 5.8 4.0 - - - +
106R GLU* 4.1 4.7 - - + +
107R ALA* 1.3 83.7 - - - +
109R GLY* 1.3 66.5 + - - +
110R GLY 3.2 0.3 + - - -
111R GLY* 2.8 27.1 + - - +
112R SER 4.4 4.9 - - - +
113R LYS* 3.9 37.0 - - + -
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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