Contacts of the helix formed by residues 88 - 101 (chain B) in PDB entry 5W4A
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 PHE 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57B VAL* 3.9 36.8 - - + -
60B ILE* 3.9 35.4 - - + -
61B VAL* 4.4 3.8 - - + -
81B LEU* 3.6 45.6 - - + +
84B LEU* 3.4 46.7 - - + -
85B GLY 3.0 2.2 + - - +
86B PRO 3.0 1.0 - - - -
87B ASP* 1.3 95.0 - - + +
89B LEU* 1.3 60.0 + - - +
90B THR 3.4 2.5 - - - -
91B GLU* 3.3 10.1 + - + +
92B PHE* 3.1 24.4 + - - +
178B ILE* 5.3 2.9 - - + -
179B LEU* 5.6 2.0 - - + -
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Residues in contact with LEU 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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81B LEU 5.7 0.7 - - - +
82B LEU* 4.2 26.2 - - + -
85B GLY 3.5 9.0 + - - +
86B PRO* 3.3 21.6 + - + +
88B PHE* 1.3 75.4 - - - +
90B THR* 1.3 67.1 + - - +
92B PHE* 3.2 13.3 + - + +
93B LYS* 3.0 37.6 + - + +
111B LEU* 5.9 3.6 - - + +
112B ALA* 5.2 8.5 - - + +
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Residues in contact with THR 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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86B PRO 4.7 1.8 + - - -
87B ASP 5.3 2.8 - - - -
88B PHE* 3.4 0.4 - - - +
89B LEU* 1.3 77.7 - - - +
91B GLU* 1.3 63.3 + - - +
93B LYS* 3.3 10.3 + - + +
94B LYS* 3.1 48.3 + - + +
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Residues in contact with GLU 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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57B VAL* 6.0 2.6 - - + +
58B ASP* 5.3 3.3 - - - +
61B VAL* 3.7 31.1 - - + +
65B PHE* 4.7 0.2 - - + -
81B LEU* 3.8 18.8 - - + -
87B ASP 5.7 0.6 + - - +
88B PHE* 3.3 14.4 + - + +
89B LEU 3.2 0.6 - - - -
90B THR* 1.3 77.5 - - - +
92B PHE* 1.3 64.2 + - - +
94B LYS* 3.3 18.2 + - - +
95B ARG* 2.8 66.2 + - - +
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Residues in contact with PHE 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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78B MSE 3.5 43.2 - - + +
81B LEU* 3.6 14.1 - - + +
82B LEU* 3.5 39.0 - - + -
88B PHE 3.1 13.7 + - - +
89B LEU* 3.2 16.4 + - + +
91B GLU* 1.3 76.2 - - - +
93B LYS* 1.3 61.2 + - + +
95B ARG* 3.2 2.2 + - - -
96B ASN* 2.9 35.0 + - + +
106B HIS* 3.7 32.5 - + + -
108B LEU 4.7 6.3 - - - -
109B SER* 4.8 2.7 - - - -
111B LEU* 5.9 0.2 - - + -
112B ALA* 3.7 30.3 - - + -
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Residues in contact with LYS 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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89B LEU* 3.0 29.3 + - + +
90B THR* 3.8 8.1 - - + +
91B GLU 3.3 0.2 - - - -
92B PHE* 1.3 78.8 - - + +
94B LYS* 1.3 58.4 + - + +
96B ASN* 3.3 4.8 + - - +
97B GLN* 2.9 30.2 + - - +
112B ALA* 3.5 40.3 + - + +
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Residues in contact with LYS 94 (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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90B THR* 3.1 38.9 + - + +
91B GLU* 3.7 20.6 + - - +
93B LYS* 1.3 74.6 - - + +
95B ARG* 1.3 65.9 + - - +
97B GLN* 3.3 11.5 + - - +
98B ASP* 3.0 31.2 + - - +
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Residues in contact with ARG 95 (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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61B VAL* 3.6 12.1 - - - +
65B PHE* 3.5 61.7 + - + +
69B SER* 6.4 0.2 - - - -
74B ILE* 4.7 10.8 - - + +
78B MSE 3.8 19.7 - - + -
81B LEU* 4.4 0.9 - - + -
91B GLU* 2.8 47.0 + - - +
92B PHE 3.7 3.6 - - - +
94B LYS* 1.3 77.6 - - + +
96B ASN* 1.3 63.5 + - - +
98B ASP* 3.3 10.0 + - - +
99B LEU* 3.1 26.5 + - - +
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Residues in contact with ASN 96 (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 MSE 3.4 15.4 - - + +
92B PHE* 2.9 23.9 + - + +
93B LYS* 3.6 7.4 - - - +
95B ARG* 1.3 75.1 - - - +
97B GLN* 1.3 65.4 + - - +
99B LEU* 3.2 14.0 + - - +
100B ALA* 3.3 12.0 + - - +
104B LEU 4.6 1.2 - - - +
105B THR* 3.3 13.3 + - - -
106B HIS* 2.9 26.6 + - - -
109B SER* 2.8 30.2 + - - +
112B ALA* 5.2 3.2 - - + +
113B GLN* 3.8 12.1 - - - +
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Residues in contact with GLN 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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93B LYS 2.9 17.4 + - - +
94B LYS* 3.3 12.0 + - - +
96B ASN* 1.3 77.2 - - - +
98B ASP* 1.3 87.4 + - - +
100B ALA* 3.3 20.0 + - - +
101B ARG* 4.1 9.0 + - - +
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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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94B LYS* 3.0 14.9 + - - +
95B ARG* 3.7 10.3 - - - +
97B GLN* 1.3 107.8 + - - +
99B LEU* 1.3 62.8 + - + +
100B ALA 3.4 0.3 + - - -
101B ARG* 3.5 31.1 + - - +
102B PHE* 3.5 18.7 - - + -
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Residues in contact with LEU 99 (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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71B SER* 5.3 3.4 - - - +
74B ILE* 4.0 31.2 - - + -
75B LEU* 3.7 22.4 - - + -
78B MSE 3.6 28.0 - - - -
95B ARG 3.1 15.4 + - - +
96B ASN* 3.2 15.4 + - - +
98B ASP* 1.3 76.5 - - + +
100B ALA* 1.3 66.2 + - - +
102B PHE* 2.9 23.4 + - + +
104B LEU* 3.2 48.7 + - + +
105B THR* 4.5 4.7 - - - -
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Residues in contact with ALA 100 (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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96B ASN 3.3 8.6 + - - +
97B GLN* 3.3 15.1 + - - +
98B ASP 3.2 1.0 - - - -
99B LEU* 1.3 78.3 - - - +
101B ARG* 1.3 57.8 + - + +
103B ASN* 2.9 23.4 + - - +
104B LEU 3.5 10.3 - - - +
105B THR* 6.3 0.7 - - - -
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Residues in contact with ARG 101 (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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97B GLN* 4.4 9.9 - - - +
98B ASP* 3.7 27.9 + - - +
99B LEU 3.1 0.8 - - - -
100B ALA* 1.3 76.8 - - + +
102B PHE* 1.3 92.6 + - + +
103B ASN* 3.4 5.0 + - - +
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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