Contacts of the helix formed by residues 83 - 107 (chain w) in PDB entry 5Z58
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 GLU 83 (chain w).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68w ARG* 4.8 17.7 - - + -
82w ALA* 1.3 78.0 - - - +
84w PHE* 1.3 66.8 + - - +
86w ASN* 3.2 6.5 + - - +
87w ARG* 2.9 26.9 + - - +
156w GLU* 6.5 0.9 - - + -
371w ASP* 3.5 28.6 + - + +
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Residues in contact with PHE 84 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31w SER* 5.7 8.7 - - - -
32w THR* 5.5 14.3 - - - +
68w ARG* 5.2 15.5 - - + +
82w ALA 4.4 3.3 - - - +
83w GLU* 1.3 79.1 - - - +
85w TYR* 1.3 57.4 + - - +
87w ARG* 3.5 4.8 + - - +
88w LEU* 2.9 28.7 + - - +
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Residues in contact with TYR 85 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82w ALA* 3.7 11.9 + - - +
83w GLU 3.3 0.2 - - - -
84w PHE* 1.3 77.4 - - - +
86w ASN* 1.3 69.3 + - - +
88w LEU* 2.9 16.3 + - - +
89w LYS* 2.9 13.2 + - - +
166w ILE* 6.0 5.2 - - + -
176w GLU* 4.6 24.2 - - + +
177w ARG* 6.2 0.2 - - + -
251w SER 6.1 0.9 - - - +
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Residues in contact with ASN 86 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82w ALA 2.9 20.2 + - - +
83w GLU* 3.2 8.7 + - - +
85w TYR* 1.3 73.8 - - - +
87w ARG* 1.3 65.3 + - - +
89w LYS* 2.8 20.5 + - - +
90w GLN* 2.9 12.1 + - - +
166w ILE* 5.6 10.6 - - + +
371w ASP* 4.8 11.2 - - + -
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Residues in contact with ARG 87 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25w GLU* 5.6 10.5 - - + -
32w THR* 5.7 7.9 - - - -
83w GLU 2.9 14.6 + - - +
84w PHE* 3.9 4.5 - - - +
86w ASN* 1.3 76.9 - - - +
88w LEU* 1.3 56.6 + - - +
90w GLN* 3.5 8.9 - - - +
91w ILE* 2.8 30.7 + - - +
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Residues in contact with LEU 88 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32w THR* 5.7 9.8 - - - +
84w PHE 2.9 14.6 + - - +
85w TYR* 2.9 14.8 + - - +
87w ARG* 1.3 77.5 - - - +
89w LYS* 1.3 57.4 + - - +
91w ILE* 3.6 6.0 + - - +
92w LYS* 2.9 24.8 + - - +
253w GLU* 3.8 15.7 - - + +
254w GLU* 4.7 15.6 + - + +
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Residues in contact with LYS 89 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85w TYR 2.9 9.1 + - - +
86w ASN* 2.8 14.5 + - - +
88w LEU* 1.3 70.9 - - - +
90w GLN* 1.3 63.4 + - - +
92w LYS* 2.9 25.5 - - + +
93w GLU* 3.0 9.7 + - - +
164w LEU* 6.3 2.7 - - + -
253w GLU* 4.2 9.3 - - + +
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Residues in contact with GLN 90 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86w ASN 2.9 11.7 + - - +
87w ARG* 3.5 12.8 - - - +
89w LYS* 1.3 75.6 - - - +
91w ILE* 1.3 57.5 + - - +
93w GLU* 3.1 6.7 + - - +
94w PHE* 2.9 27.0 + - - +
157w LYS* 6.3 3.8 - - + -
158w LEU* 6.1 4.3 - - + +
161w ILE* 4.9 20.2 - - + +
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Residues in contact with ILE 91 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22w MET* 4.6 18.6 - - + +
25w GLU* 6.2 2.9 - - + -
87w ARG 2.8 17.2 + - - +
88w LEU* 3.7 7.9 - - - +
90w GLN* 1.3 75.3 - - - +
92w LYS* 1.3 57.0 + - - +
94w PHE* 3.3 9.5 + - - +
95w HIS* 2.9 30.8 + - - +
254w GLU* 6.3 2.7 - - + -
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Residues in contact with LYS 92 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88w LEU 2.9 15.2 + - - +
89w LYS* 2.9 19.5 - - - +
91w ILE* 1.3 77.1 - - - +
93w GLU* 1.3 60.7 + - - +
95w HIS* 3.2 8.1 + - - +
96w ARG* 3.0 20.1 + - - +
253w GLU* 4.0 20.6 - - + +
254w GLU* 5.9 2.2 - - - +
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Residues in contact with GLU 93 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89w LYS 3.0 11.8 + - - +
90w GLN* 3.8 7.9 - - - +
92w LYS* 1.3 75.4 - - - +
94w PHE* 1.3 62.6 + - - +
96w ARG* 3.0 11.6 + - + +
97w LYS* 2.9 22.4 + - - +
161w ILE* 5.4 9.9 - - + -
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Residues in contact with PHE 94 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18w LEU* 4.9 15.3 - - + +
21w VAL* 6.3 2.5 - - + -
22w MET* 5.3 9.6 - - + -
90w GLN 2.9 14.4 + - - +
91w ILE* 3.4 14.4 - - - +
93w GLU* 1.3 75.6 - - - +
95w HIS* 1.3 56.5 + - - +
97w LYS* 3.1 9.6 + - - +
98w HIS* 2.9 28.9 + - - +
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Residues in contact with HIS 95 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239u VAL* 6.3 3.4 - - + -
91w ILE 2.9 16.7 + - - +
92w LYS* 3.2 6.7 + - - +
94w PHE* 1.3 75.0 - - - +
96w ARG* 1.3 57.2 + - - +
98w HIS* 3.6 8.6 - - - +
99w PRO* 2.9 29.1 - - - +
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Residues in contact with ARG 96 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92w LYS 3.0 12.2 + - - +
93w GLU* 3.0 14.8 + - - +
95w HIS* 1.3 74.4 - - - +
97w LYS* 1.3 66.8 + - - +
99w PRO* 3.1 8.0 - - - +
100w ASN* 2.9 23.1 + - - +
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Residues in contact with LYS 97 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18w LEU* 6.1 2.2 - - + -
93w GLU 2.9 11.2 + - - +
94w PHE* 3.3 11.4 - - - +
96w ARG* 1.3 75.1 - - - +
98w HIS* 1.3 63.1 + - - +
100w ASN* 3.0 9.9 + - - +
101w GLU* 2.9 23.5 + - - +
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Residues in contact with HIS 98 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15w LYS* 5.7 11.0 - - + +
18w LEU* 4.9 15.6 - - + +
94w PHE 2.9 13.4 + - - +
95w HIS* 3.6 12.6 - - - +
97w LYS* 1.3 76.7 - - - +
99w PRO* 1.3 57.0 - - - +
101w GLU* 3.3 6.1 + - - +
102w ILE* 2.9 31.3 + - - +
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Residues in contact with PRO 99 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95w HIS 2.9 18.4 - - - +
96w ARG* 3.5 6.7 - - - +
98w HIS* 1.3 75.1 - - - +
100w ASN* 1.3 63.3 + - - +
102w ILE* 3.5 7.1 + - + +
103w CYS* 3.0 22.7 + - - +
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Residues in contact with ASN 100 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96w ARG 2.9 12.5 + - - +
97w LYS* 3.3 11.9 - - - +
99w PRO* 1.3 76.5 - - - +
101w GLU* 1.3 63.1 + - - +
103w CYS* 2.9 17.6 + - - +
104w VAL* 3.0 15.7 + - - +
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Residues in contact with GLU 101 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11w TYR* 5.0 19.0 - - + +
14w GLU* 5.8 5.2 - - + -
15w LYS* 5.6 8.5 - - + +
97w LYS 2.9 18.3 + - - +
98w HIS* 3.8 6.5 - - - +
100w ASN* 1.3 73.1 - - - +
102w ILE* 1.3 63.9 + - - +
104w VAL* 3.3 5.3 + - - +
105w PRO* 2.9 27.0 - - - +
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Residues in contact with ILE 102 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229u LEU* 5.0 20.5 - - + +
231u LYS 6.2 0.2 - - - +
15w LYS* 6.2 1.2 - - + +
98w HIS 2.9 17.9 + - - +
99w PRO* 3.6 7.9 - - + +
101w GLU* 1.3 74.8 - - - +
103w CYS* 1.3 57.9 + - - +
105w PRO* 3.5 6.0 - - - +
106w MET* 3.0 28.9 + - - +
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Residues in contact with CYS 103 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99w PRO 3.0 13.2 + - - +
100w ASN* 2.9 14.1 + - - +
102w ILE* 1.3 74.0 - - - +
104w VAL* 1.3 67.3 + - - +
106w MET* 2.9 18.7 + - - +
107w SER* 3.0 13.2 + - - -
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Residues in contact with VAL 104 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100w ASN 3.0 14.0 + - - +
101w GLU* 4.0 7.4 - - - +
103w CYS* 1.3 71.9 - - - +
105w PRO* 1.3 63.7 - - - +
107w SER* 3.0 25.7 + - - -
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Residues in contact with PRO 105 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8w GLN* 5.9 6.9 - - + +
11w TYR* 4.5 18.6 - - + -
101w GLU 2.9 18.9 - - - +
102w ILE* 3.5 7.4 - - - +
104w VAL* 1.3 78.3 - - - +
106w MET* 1.3 62.9 + - - +
107w SER 3.2 4.2 + - - -
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Residues in contact with MET 106 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228u LYS* 4.3 27.4 - - + +
229u LEU 5.2 6.5 - - - +
102w ILE 3.0 14.1 + - - +
103w CYS* 2.9 11.9 + - - +
105w PRO* 1.3 76.1 - - - +
107w SER* 1.3 60.1 + - - +
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Residues in contact with SER 107 (chain w).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103w CYS 3.0 10.7 + - - -
104w VAL* 3.0 22.2 + - - -
105w PRO 4.0 4.0 - - - -
106w MET* 1.3 82.7 - - - +
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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
------------------------------------------------------------
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