Contacts of the helix formed by residues 90 - 110 (chain S) in PDB entry 3H1J
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 LEU 90 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34S ASP* 2.8 21.2 + - - +
37S LEU* 4.1 16.2 - - + -
43S VAL* 4.0 27.6 - - + -
46S ALA* 3.3 42.4 - - + +
47S LEU* 3.7 18.2 - - + +
50S LEU* 4.1 14.6 - - + -
58S ARG* 5.4 0.9 - - - +
89S TYR* 1.3 86.7 - - + +
91S GLU* 1.3 65.7 + - - +
92S PRO* 3.2 4.5 - - - -
93S TYR* 2.8 21.0 + - + +
94S LEU* 2.9 16.3 + - + -
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Residues in contact with GLU 91 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379P ASN* 3.8 14.6 + - - +
380P TYR* 3.5 25.8 - - - -
33S ARG* 3.5 35.8 + - - +
34S ASP* 2.7 11.5 + - - -
88S PRO* 3.5 12.8 - - + +
90S LEU* 1.3 70.6 - - - +
92S PRO* 1.3 65.6 - - + +
94S LEU* 3.3 12.1 + - - +
95S LYS* 2.9 54.0 + - - +
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Residues in contact with PRO 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88S PRO* 3.1 18.4 - - + +
89S TYR* 4.2 7.6 - - - +
90S LEU 3.2 2.7 - - - +
91S GLU* 1.3 91.1 - - + +
93S TYR* 1.3 77.3 + - + +
95S LYS* 2.9 25.4 + - + +
96S GLU* 3.1 13.0 + - - +
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Residues in contact with TYR 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B TRP* 3.9 29.7 - + - -
46S ALA* 4.2 10.8 - - + -
49S ARG* 3.9 25.2 + - + +
50S LEU* 3.6 19.3 - - + -
51S PRO* 3.0 30.6 - - + +
54S LEU* 4.9 4.6 - - + +
89S TYR 3.3 27.1 - - - -
90S LEU* 2.8 19.8 + - + +
92S PRO* 1.3 79.9 - - + +
94S LEU* 1.3 64.1 + - - +
96S GLU* 3.1 9.6 + - - +
97S VAL* 2.9 25.0 + - - +
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Residues in contact with LEU 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312P LYS* 6.1 4.9 - - + -
380P TYR* 5.5 5.4 - - + -
37S LEU* 3.6 32.5 - - + -
42S ASP* 3.8 28.9 - - + +
43S VAL* 4.0 13.0 - - + +
46S ALA* 4.0 11.4 - - + +
90S LEU* 2.9 13.6 + - + +
91S GLU* 3.3 14.6 - - - +
93S TYR* 1.3 78.1 - - - +
95S LYS* 1.3 63.9 + - - +
97S VAL* 3.3 2.8 + - + +
98S ILE* 3.0 54.9 + - + +
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Residues in contact with LYS 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91S GLU* 2.9 47.7 + - + +
92S PRO* 2.9 13.0 + - + +
94S LEU* 1.3 78.2 - - - +
96S GLU* 1.3 52.5 + - - +
98S ILE* 3.1 7.6 + - - +
99S ARG* 2.7 37.7 + - - +
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Residues in contact with GLU 96 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ARG* 2.9 36.4 + - - +
135B TRP* 5.6 2.5 - - + -
49S ARG* 4.1 7.2 - - - +
92S PRO 3.1 6.7 + - - +
93S TYR* 3.4 10.1 - - - +
95S LYS* 1.3 79.5 - - - +
97S VAL* 1.3 53.9 + - - +
99S ARG* 2.6 46.3 + - - +
100S GLU* 2.6 58.2 + - - +
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Residues in contact with VAL 97 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S ASP* 3.5 41.3 - - + +
45S GLU* 3.5 31.2 - - + -
46S ALA* 4.0 14.4 - - - +
49S ARG* 3.6 20.4 - - - +
93S TYR 2.9 15.4 + - - +
94S LEU* 3.5 8.5 - - - +
96S GLU* 1.3 75.2 - - - +
98S ILE* 1.3 58.9 + - - +
100S GLU* 3.3 11.0 + - - +
101S ARG* 3.0 28.1 + - + +
104S ARG* 4.8 2.3 + - - +
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Residues in contact with ILE 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312P LYS* 6.2 4.0 - - - -
42S ASP* 3.6 25.6 - - + +
94S LEU* 3.0 39.0 + - + +
95S LYS* 3.5 7.2 - - - +
97S VAL* 1.3 74.4 - - - +
99S ARG* 1.3 66.4 + - - +
101S ARG* 3.4 24.1 + - - +
102S LEU* 3.0 35.8 + - + +
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Residues in contact with ARG 99 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ARG* 4.8 3.8 - - - +
95S LYS* 2.7 18.0 + - - +
96S GLU* 2.6 46.9 + - - +
98S ILE* 1.3 73.1 - - - +
100S GLU* 1.3 63.3 + - - +
102S LEU* 3.2 12.2 + - - +
103S GLU* 3.2 21.5 + - - +
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Residues in contact with GLU 100 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B THR* 5.1 2.3 - - - +
81B SER* 5.8 6.7 - - - -
133B ARG* 2.7 30.2 + - - -
136B GLU* 4.4 4.2 - - - +
49S ARG* 2.6 39.9 + - - -
96S GLU* 2.6 31.4 + - - +
97S VAL* 3.4 10.6 - - - +
99S ARG* 1.3 74.9 - - - +
101S ARG* 1.3 61.4 + - - +
103S GLU* 3.3 16.8 + - - +
104S ARG* 3.2 38.0 + - - +
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Residues in contact with ARG 101 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42S ASP* 2.4 43.5 + - - +
97S VAL* 3.0 15.5 + - + +
98S ILE* 3.7 18.5 - - - +
100S GLU* 1.3 74.0 - - - +
102S LEU* 1.3 87.6 + - - +
104S ARG* 3.1 34.8 + - - +
105S GLU* 2.8 52.8 + - + +
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Residues in contact with LEU 102 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98S ILE* 3.0 31.7 + - + +
99S ARG* 3.5 8.7 - - - +
101S ARG* 1.3 98.9 - - - +
103S GLU* 1.3 57.8 + - - +
105S GLU* 3.2 17.6 + - - +
106S ALA* 2.8 31.1 + - - +
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Residues in contact with GLU 103 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B SER* 3.0 32.6 + - - -
83B PHE* 4.2 16.9 - - + +
84B ARG* 3.8 20.8 - - - -
99S ARG 3.2 8.7 + - - +
100S GLU* 3.4 15.9 - - - +
101S ARG 3.1 0.4 - - - -
102S LEU* 1.3 74.7 - - - +
104S ARG* 1.3 69.4 + - - +
106S ALA* 3.1 6.5 + - - +
107S TRP* 2.8 34.2 + - + +
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Residues in contact with ARG 104 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288A LYS* 6.0 1.2 - - - +
289A HIS* 4.5 15.4 - - - -
83B PHE* 3.6 46.6 - - + +
49S ARG* 5.7 1.6 - - - +
97S VAL* 4.8 2.4 + - - +
100S GLU* 3.2 27.9 + - - +
101S ARG* 3.1 42.7 + - - +
103S GLU* 1.3 79.0 - - - +
105S GLU* 1.3 54.8 + - + +
107S TRP* 3.0 1.6 + - - +
108S ASN* 2.6 49.4 + - - +
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Residues in contact with GLU 105 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101S ARG* 2.8 51.2 + - + +
102S LEU* 3.3 23.0 - - + +
104S ARG* 1.3 79.4 - - + +
106S ALA* 1.3 63.1 + - - +
108S ASN* 3.2 12.4 + - - +
109S LYS* 3.0 40.1 + - - +
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Residues in contact with ALA 106 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102S LEU 2.8 19.0 + - - +
103S GLU* 3.7 4.9 - - - +
105S GLU* 1.3 74.2 - - - +
107S TRP* 1.3 61.8 + - - +
109S LYS* 3.3 11.6 + - - +
110S LYS* 3.2 23.4 + - - +
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Residues in contact with TRP 107 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B PHE* 3.8 27.6 - + + -
84B ARG* 3.7 38.8 - - + -
87B ARG* 4.0 33.9 + - + +
88B GLY* 4.2 15.0 - - - -
91B ALA* 5.1 8.6 - - + +
122B TYR* 4.5 2.9 - - - -
103S GLU* 2.8 26.8 + - + +
104S ARG 3.3 4.3 - - - +
106S ALA* 1.3 78.8 - - - +
108S ASN* 1.3 58.5 + - - +
110S LYS* 3.0 35.4 - - + +
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Residues in contact with ASN 108 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B PHE* 4.2 2.0 - - - -
87B ARG* 3.2 31.2 + - - -
104S ARG* 2.6 44.8 + - - +
105S GLU* 3.7 7.7 - - - +
107S TRP* 1.3 71.8 - - - +
109S LYS* 1.3 63.8 + - + +
110S LYS* 4.4 3.0 - - - +
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Residues in contact with LYS 109 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105S GLU* 3.0 38.8 + - - +
106S ALA* 3.8 9.4 - - - +
107S TRP 3.3 0.2 - - - -
108S ASN* 1.3 77.0 - - + +
110S LYS* 1.3 64.7 - - - +
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Residues in contact with LYS 110 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A SER* 3.2 28.9 + - - -
106S ALA 3.2 12.3 + - - +
107S TRP* 3.0 31.9 + - + +
108S ASN 4.4 3.5 - - - +
109S LYS* 1.3 83.1 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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