Contacts of the helix formed by residues 95 - 109 (chain B) in PDB entry 5WZF
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 95 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TRP* 4.2 2.2 - - - +
46A THR* 3.7 27.6 - - - +
50A ARG* 5.6 1.3 - - - -
43B GLU* 4.9 6.7 + - - -
86B LEU* 3.8 0.7 - - - +
94B TYR* 1.3 76.4 - - - +
96B PHE* 1.3 64.0 + - - +
97B VAL* 3.5 7.5 + - - +
98B ASP* 3.0 37.8 + - - +
99B ALA* 3.1 22.0 + - - +
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Residues in contact with PHE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN 4.6 5.8 - - - -
39A HIS* 5.5 1.1 - - - -
42A GLY* 3.3 43.5 - - - +
45A TRP* 3.6 8.4 - - + -
46A THR* 3.1 9.1 + - - +
39B HIS* 3.5 28.7 - + - -
79B GLU* 4.1 21.3 - - - -
82B ALA* 4.9 4.9 - - + -
83B TRP* 3.6 35.7 - + - -
86B LEU* 3.9 21.1 - - + -
95B SER* 1.3 71.9 - - - +
97B VAL* 1.3 71.9 + - + +
99B ALA* 3.1 3.5 + - - +
100B THR* 3.0 45.7 + - + +
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Residues in contact with VAL 97 (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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46A THR* 4.7 1.3 + - - +
5B ASP* 5.1 1.1 - - - +
6B THR* 4.6 0.2 - - - +
39B HIS* 4.2 22.0 - - + +
40B VAL* 3.9 30.7 - - + +
43B GLU* 3.3 37.2 - - + +
95B SER* 3.3 7.2 + - - +
96B PHE* 1.3 84.5 - - + +
98B ASP* 1.3 61.4 + - - +
100B THR* 2.7 21.7 + - - -
101B SER* 2.9 20.1 + - - +
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Residues in contact with ASP 98 (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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5B ASP* 3.9 17.8 - - - +
43B GLU* 5.3 1.2 - - - +
94B TYR* 4.8 3.2 - - + -
95B SER* 3.0 34.1 + - - +
97B VAL* 1.3 79.9 - - - +
99B ALA* 1.3 57.0 + - - +
101B SER* 3.0 5.8 + - - -
102B PHE* 2.8 55.8 + - + -
119B ASP* 3.5 30.2 - - - +
120B PHE* 4.0 7.6 - - - -
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Residues in contact with ALA 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B ALA* 3.9 17.0 - - + +
85B TRP* 4.0 10.8 - - + -
86B LEU* 3.5 40.2 - - + -
95B SER 3.1 6.1 + - - -
96B PHE 3.5 7.9 - - - +
98B ASP* 1.3 76.4 - - - +
100B THR* 1.3 61.6 + - - +
102B PHE* 3.5 13.7 + - - +
103B ALA* 3.1 22.2 + - - +
106B ARG* 4.9 1.7 + - - -
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Residues in contact with THR 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B SER* 4.9 1.7 + - - -
39B HIS* 4.0 25.2 - - + +
74B VAL* 4.3 11.7 - - + +
78B LEU* 4.9 0.5 - - - +
79B GLU* 4.5 7.9 - - + -
82B ALA* 3.8 14.4 - - + -
96B PHE* 3.0 44.3 + - + +
97B VAL* 2.7 24.8 + - - -
99B ALA* 1.3 75.0 - - - +
101B SER* 1.3 60.3 + - - +
103B ALA* 3.3 4.5 + - - +
104B VAL* 3.0 33.6 + - - +
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Residues in contact with SER 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 3.3 36.0 - - - -
5B ASP* 4.7 0.7 + - - -
37B SER* 4.5 1.2 + - - -
40B VAL* 3.5 13.9 - - - +
97B VAL* 2.9 18.5 + - - +
98B ASP* 3.0 9.3 + - - -
100B THR* 1.3 75.2 + - - +
102B PHE* 1.3 66.5 + - - +
104B VAL* 3.2 4.4 + - - +
105B MET* 3.0 28.4 + - - +
120B PHE* 3.6 18.5 - - - -
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Residues in contact with PHE 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B TRP* 3.6 34.5 - + + -
94B TYR* 3.7 13.2 - + - -
98B ASP* 2.8 37.8 + - + +
99B ALA* 3.7 7.4 - - - +
101B SER* 1.3 74.8 - - - +
103B ALA* 1.3 58.6 + - - +
105B MET* 3.3 1.4 + - - -
106B ARG* 3.0 49.4 + - - +
119B ASP 3.7 13.2 - - - -
120B PHE* 3.5 37.2 - + - -
123B ALA* 3.5 25.6 - - + -
125B PHE* 3.6 26.7 - + + -
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Residues in contact with ALA 103 (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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78B LEU* 3.7 36.8 - - + +
81B GLN* 3.8 4.0 - - - +
82B ALA* 4.7 3.6 - - + +
99B ALA 3.1 16.4 + - - +
100B THR* 3.6 8.1 - - - +
101B SER 3.2 0.2 - - - -
102B PHE* 1.3 75.3 - - - +
104B VAL* 1.3 59.3 + - - +
106B ARG* 3.5 25.4 + - - +
107B LYS* 3.0 28.2 + - - +
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 3.7 27.8 - - + -
35B MET* 4.1 19.3 - - - -
37B SER* 4.7 2.5 - - - -
72B GLU* 4.2 17.7 - - + -
74B VAL* 3.9 19.7 - - + -
78B LEU* 3.7 21.8 - - + -
100B THR 3.0 21.1 + - - +
101B SER* 3.6 7.4 - - - +
103B ALA* 1.3 76.4 - - - +
105B MET* 1.3 57.2 + - - +
107B LYS* 3.2 3.1 + - + +
108B LYS* 2.8 33.0 + - + +
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Residues in contact with MET 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B PHE* 3.6 25.4 - - + -
101B SER 3.0 16.8 + - - +
102B PHE 3.3 4.9 + - - +
104B VAL* 1.3 77.4 - - - +
106B ARG* 1.3 59.0 + - - +
109B GLY* 2.8 25.8 + - - -
110B ILE* 2.8 37.7 + - + +
111B GLN 3.7 9.0 - - - +
112B ASN 3.7 25.8 - - - +
113B ALA* 3.9 4.3 - - + -
120B PHE* 3.6 33.7 - - - -
125B PHE* 3.5 33.2 - - + -
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Residues in contact with ARG 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B GLN* 2.9 36.6 + - - +
85B TRP* 3.7 37.0 - - - +
99B ALA 4.9 1.4 + - - -
102B PHE* 3.0 37.7 + - - +
103B ALA* 3.6 21.4 - - - +
105B MET* 1.3 77.0 - - - +
107B LYS* 1.3 62.1 + - - +
109B GLY* 3.5 8.5 + - - -
125B PHE* 4.1 16.3 - - + -
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Residues in contact with LYS 107 (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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72B GLU* 3.1 25.7 + - - +
75B THR* 4.6 16.6 + - - +
78B LEU* 4.1 26.9 - - + +
103B ALA 3.0 19.0 + - - +
104B VAL* 3.2 4.9 + - - +
106B ARG* 1.3 79.5 - - - +
108B LYS* 1.3 81.4 + - + +
109B GLY 3.6 0.3 + - - -
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Residues in contact with LYS 108 (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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35B MET* 3.6 30.9 - - + +
72B GLU* 3.5 33.2 + - - -
104B VAL* 2.8 22.2 + - + +
107B LYS* 1.3 98.5 - - + +
109B GLY* 1.3 62.5 + - - +
110B ILE* 3.3 23.3 + - + +
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Residues in contact with GLY 109 (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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1B SER* 4.9 2.1 + - - -
105B MET 2.8 6.7 + - - -
106B ARG* 3.5 7.2 + - - -
107B LYS 3.3 3.8 + - - -
108B LYS* 1.3 79.0 - - - +
110B ILE* 1.3 61.4 + - - +
111B GLN* 3.9 2.3 + - - +
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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