Contacts of the helix formed by residues 87 - 103 (chain Z) in PDB entry 5WTI
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 ASP 87 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86Z VAL* 1.3 80.6 - - + +
88Z LYS* 1.3 74.6 + - - +
89Z ASP* 3.5 18.5 + - - +
90Z VAL* 3.6 22.3 + - + +
91Z VAL* 3.3 21.5 + - - +
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Residues in contact with LYS 88 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Z GLN 5.8 0.2 + - - -
67Z ALA* 6.3 0.6 - - - +
70Z TRP* 3.6 57.8 - - + +
86Z VAL 4.7 0.9 - - - +
87Z ASP* 1.3 78.6 + - - +
89Z ASP* 1.3 59.0 + - - +
91Z VAL* 2.9 4.2 + - - +
92Z PHE* 2.5 64.8 + - + +
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Residues in contact with ASP 89 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87Z ASP* 3.5 12.9 + - - +
88Z LYS* 1.3 79.5 - - - +
90Z VAL* 1.3 58.3 + - + +
92Z PHE* 4.0 18.8 - - - +
93Z ASN* 2.8 43.3 + - - +
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Residues in contact with VAL 90 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86Z VAL* 4.4 7.0 - - + -
87Z ASP* 3.6 23.5 + - + +
88Z LYS 3.2 0.2 - - - -
89Z ASP* 1.3 78.8 - - + +
91Z VAL* 1.3 61.9 + - - +
93Z ASN* 3.4 7.5 + - - +
94Z ILE* 3.3 22.5 + - - +
181Z TYR* 3.0 37.5 - - + +
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Residues in contact with VAL 91 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70Z TRP* 3.9 23.3 - - + -
73Z VAL* 4.2 6.5 - - + -
77Z GLN* 5.4 0.7 - - - +
86Z VAL* 3.7 25.8 - - + -
87Z ASP 3.3 14.8 + - - +
88Z LYS 2.9 7.0 + - - +
90Z VAL* 1.3 73.9 - - - +
92Z PHE* 1.3 66.8 + - + +
94Z ILE* 3.2 9.3 - - + +
95Z LEU* 3.2 42.0 + - + +
181Z TYR* 3.9 15.3 - - + -
183Z LEU* 3.9 19.3 - - + -
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Residues in contact with PHE 92 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43Z GLN* 2.9 34.9 + - - +
66Z GLN* 3.4 59.0 - - + +
69Z LEU* 3.8 26.2 - - + -
70Z TRP* 4.1 21.1 - + + -
88Z LYS* 2.5 49.5 + - + +
89Z ASP* 3.6 21.8 - - - +
91Z VAL* 1.3 76.1 - - + +
93Z ASN* 1.3 64.5 + - - +
95Z LEU* 4.9 0.2 - - - -
96Z ARG* 3.2 8.3 + - - +
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Residues in contact with ASN 93 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89Z ASP* 2.8 32.6 + - - +
90Z VAL* 3.9 7.3 - - - +
92Z PHE* 1.3 82.5 - - - +
94Z ILE* 1.3 57.0 + - - +
96Z ARG* 3.4 5.1 + - - +
97Z GLU* 2.9 30.5 + - - +
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Residues in contact with ILE 94 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90Z VAL 3.3 10.6 + - - +
91Z VAL* 3.2 18.2 - - + +
93Z ASN* 1.3 78.9 - - - +
95Z LEU* 1.3 61.8 + - + +
97Z GLU* 3.4 15.7 + - - +
98Z LEU* 2.9 26.5 + - - +
173Z LYS* 4.8 6.3 - - - -
174Z ILE* 3.9 42.9 - - + +
177Z LYS* 4.1 26.7 - - + -
178Z LEU* 4.1 17.9 - - + -
181Z TYR* 4.1 15.5 - - + -
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Residues in contact with LEU 95 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41Z ILE* 4.0 20.3 - - + +
43Z GLN* 3.5 11.4 - - - +
69Z LEU* 3.7 33.7 - - + -
73Z VAL* 4.0 9.0 - - + -
91Z VAL* 3.2 32.8 + - + +
94Z ILE* 1.3 77.6 - - + +
96Z ARG* 1.3 60.6 + - - +
98Z LEU* 3.0 8.6 + - + +
99Z TYR* 2.7 29.1 + - - +
178Z LEU* 3.9 17.7 - - + -
183Z LEU* 4.6 1.3 - - + -
186Z LEU* 3.8 33.0 - - + -
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Residues in contact with ARG 96 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Z ILE 3.7 7.6 - - - -
42Z ARG* 2.8 52.2 + - - +
43Z GLN* 3.4 10.8 - - - +
44Z GLU* 4.1 22.3 + - - +
92Z PHE 3.2 17.5 + - - +
93Z ASN* 3.8 5.2 - - - +
95Z LEU* 1.3 78.2 - - - +
97Z GLU* 1.3 62.8 + - - +
99Z TYR* 3.2 7.6 + - - +
100Z GLU* 2.6 63.8 + - - +
106Z SER* 4.3 19.8 + - - -
107Z VAL* 4.9 1.0 - - - +
231Z GLU* 5.3 0.4 + - - -
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Residues in contact with GLU 97 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93Z ASN 2.9 18.4 + - - +
94Z ILE* 3.6 13.0 - - - +
96Z ARG* 1.3 77.0 - - - +
98Z LEU* 1.3 61.0 + - - +
100Z GLU* 3.6 11.3 + - - +
101Z GLU* 3.5 22.3 + - + +
170Z PRO* 3.7 13.8 - - + +
173Z LYS* 3.2 36.0 + - - -
174Z ILE* 3.6 23.4 - - + +
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Residues in contact with LEU 98 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41Z ILE* 4.7 8.5 - - + -
94Z ILE 2.9 15.3 + - - +
95Z LEU* 3.0 12.1 + - + +
97Z GLU* 1.3 75.1 - - - +
99Z TYR* 1.3 65.2 + - - +
101Z GLU* 3.1 3.4 + - - +
102Z LEU* 3.0 25.7 + - + +
120Z PHE* 4.3 21.1 - - + -
124Z LEU* 3.8 34.1 - - + -
171Z LEU* 5.0 2.9 - - + -
174Z ILE* 4.0 25.7 - - + +
178Z LEU* 4.2 9.0 - - + -
186Z LEU* 3.6 31.6 - - + -
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Residues in contact with TYR 99 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Z LEU* 3.7 29.8 - - + -
41Z ILE* 3.8 27.3 - - + +
42Z ARG* 3.2 24.3 - - + -
95Z LEU 2.7 16.5 + - - +
96Z ARG* 3.2 27.8 + - - +
98Z LEU* 1.3 75.4 - - - +
100Z GLU* 1.3 58.1 + - - +
102Z LEU* 3.0 4.3 + - - +
103Z VAL* 2.8 48.6 + - + +
106Z SER* 3.8 16.4 - - - -
227Z PHE* 3.4 15.9 - + - -
231Z GLU* 2.4 43.4 + - - +
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Residues in contact with GLU 100 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96Z ARG* 2.6 57.2 + - - +
97Z GLU* 4.1 8.6 - - - +
98Z LEU 3.3 0.4 - - - -
99Z TYR* 1.3 75.7 - - + +
101Z GLU* 1.3 66.1 + - - +
103Z VAL 4.2 1.3 - - - -
104Z PRO* 3.7 19.8 - - - +
106Z SER* 3.9 10.3 - - - +
107Z VAL* 3.5 38.0 - - + +
109Z LYS* 5.8 0.7 - - - +
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Residues in contact with GLU 101 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97Z GLU* 3.5 15.8 + - + +
98Z LEU* 3.1 10.1 + - - +
100Z GLU* 1.3 82.1 - - - +
102Z LEU* 1.3 63.0 + - - +
103Z VAL 3.4 0.2 - - - -
104Z PRO* 3.8 6.9 - - - +
109Z LYS* 5.4 6.6 + - - +
116Z LEU* 3.4 19.1 - - - +
119Z LYS* 5.0 2.9 + - - -
120Z PHE* 3.5 28.1 - - + -
169Z ASP* 4.1 6.2 - - - +
170Z PRO* 3.6 38.4 - - + +
171Z LEU* 5.7 1.3 - - - +
174Z ILE* 4.3 7.9 - - + -
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Residues in contact with LEU 102 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Z LEU* 3.7 21.5 - - + -
41Z ILE* 4.4 13.0 - - + -
98Z LEU* 3.0 17.5 + - + +
99Z TYR* 3.0 7.4 + - - +
101Z GLU* 1.3 79.7 - - - +
103Z VAL* 1.3 66.2 + - + +
104Z PRO* 3.5 0.2 - - - -
116Z LEU* 3.2 24.5 - - + +
120Z PHE* 3.5 39.5 - - + -
124Z LEU* 4.1 19.3 - - + -
187Z PHE* 6.0 0.9 - - + -
220Z PHE* 4.1 16.8 - - + -
224Z LEU* 3.7 31.1 - - + +
228Z LEU* 4.4 0.7 - - - +
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Residues in contact with VAL 103 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Z LEU* 4.6 2.5 - - + -
99Z TYR* 2.8 43.1 + - + +
100Z GLU 3.9 4.5 - - - +
102Z LEU* 1.3 83.2 - - + +
104Z PRO* 1.3 63.1 - - - +
105Z SER 3.0 5.8 + - - +
106Z SER* 2.8 22.9 + - - -
224Z LEU* 4.3 8.3 - - + -
227Z PHE* 3.7 45.1 - - + +
228Z LEU* 3.9 12.1 - - + +
231Z GLU* 3.9 17.5 - - + -
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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
------------------------------------------------------------
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