Contacts of the helix formed by residues 98 - 111 (chain B) in PDB entry 6WCW
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 THR 98 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16B ASP* 3.0 35.7 + - - +
94B ASN* 3.0 19.5 + - + +
95B THR 3.3 7.7 + - - -
97B LYS* 1.3 75.2 - - + +
99B LEU* 1.3 61.4 + - - +
100B ASP 3.5 0.7 - - - -
101B SER* 3.4 15.9 + - - -
102B TRP* 2.9 31.5 + - - -
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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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15B GLY* 6.1 0.4 - - - -
86B LEU* 4.0 31.4 - - + +
87B VAL 4.8 3.4 - - - +
88B PHE* 4.0 15.0 - - + -
95B THR 3.7 11.0 + - - +
96B PHE* 3.3 39.9 - - + +
97B LYS 3.0 3.0 + - - -
98B THR* 1.3 75.6 - - - +
100B ASP* 1.3 67.8 + - - +
102B TRP* 2.9 21.7 + - + +
103B ARG* 3.2 13.2 + - - +
122B VAL* 3.9 17.7 - - + -
142B TRP* 3.7 39.0 - - + -
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Residues in contact with ASP 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LYS 4.0 9.4 + - - +
98B THR 3.5 0.2 - - - -
99B LEU* 1.3 76.6 - - - +
101B SER* 1.3 62.8 + - - +
102B TRP 3.2 0.2 + - - -
103B ARG* 3.5 4.0 + - - +
104B ASP* 3.0 38.6 + - - +
142B TRP* 3.5 19.5 + - - -
146B LYS* 3.1 32.4 + - - -
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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
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938A ARG* 3.9 34.9 + - - +
97B LYS 4.9 0.2 + - - -
98B THR* 3.4 21.6 + - - +
99B LEU 3.1 1.0 - - - -
100B ASP* 1.3 79.7 - - - +
102B TRP* 1.3 67.8 + - - +
105B GLU* 3.3 24.3 + - - +
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Residues in contact with TRP 102 (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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14B LEU* 4.0 33.0 - - + +
15B GLY* 3.7 33.7 - - - -
16B ASP* 3.1 35.7 + - - +
64B THR* 5.5 3.1 - - - -
65B ALA 5.3 0.4 - - - -
66B GLY* 4.6 8.7 - - - -
70B PHE* 4.1 28.0 - + - -
78B TYR* 5.2 2.5 - - - -
86B LEU* 4.1 18.2 - - + -
95B THR 5.5 0.2 - - - -
98B THR* 2.9 30.7 + - - -
99B LEU* 2.9 13.9 + - + +
101B SER* 1.3 81.4 + - - +
103B ARG* 1.3 66.8 + - - +
105B GLU* 3.4 7.5 + - + +
106B PHE* 3.0 24.9 + - - +
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Residues in contact with ARG 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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86B LEU* 4.1 12.1 - - + +
99B LEU 3.2 9.0 + - - +
100B ASP* 4.0 7.6 - - - +
102B TRP* 1.3 76.8 - - - +
104B ASP* 1.3 79.7 + - - +
106B PHE* 2.9 13.6 + - - +
107B LEU* 3.0 22.8 + - + +
115B PRO 4.7 1.2 + - - -
116B GLU* 2.8 43.9 + - - +
120B PHE* 3.6 45.0 - - + -
142B TRP* 4.7 9.0 - - + -
146B LYS* 3.9 42.0 + - - +
147B ASN* 3.7 16.0 + - - -
149B ILE* 5.0 2.6 - - - +
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Residues in contact with ASP 104 (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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938A ARG* 3.3 24.2 + - - +
100B ASP* 3.0 28.7 + - - +
103B ARG* 1.3 94.3 + - - +
105B GLU* 1.3 60.7 + - - +
107B LEU* 3.7 9.6 + - - +
108B ILE* 3.2 30.5 + - + +
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Residues in contact with GLU 105 (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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931A ARG* 4.1 10.2 - - - -
934A ARG* 2.8 43.0 + - - +
935A LEU* 5.9 4.9 - - - +
938A ARG* 4.1 16.7 + - - +
78B TYR* 5.6 1.3 - - + -
101B SER 3.3 17.3 + - - +
102B TRP* 4.0 6.7 - - + +
103B ARG 3.2 0.6 - - - -
104B ASP* 1.3 79.3 - - - +
106B PHE* 1.3 58.7 + - - +
108B ILE* 3.1 4.1 + - - +
109B GLN* 3.0 46.3 + - + +
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Residues in contact with PHE 106 (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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12B ILE* 4.1 16.4 - - + -
14B LEU* 3.8 19.5 - - + -
78B TYR* 3.7 34.1 - + + -
81B ALA* 3.8 11.2 - - + -
84B CYS* 3.5 20.0 - - + -
102B TRP 3.0 17.1 + - - +
103B ARG* 2.9 5.2 + - - +
105B GLU* 1.3 74.0 - - - +
107B LEU* 1.3 65.6 + - + +
108B ILE 3.0 1.3 - - - -
109B GLN 3.1 0.7 + - - +
110B ALA* 2.9 49.1 + - + +
112B PRO* 5.6 1.3 - - + -
118B PHE* 3.2 39.9 - + - -
120B PHE* 3.6 19.1 - + - -
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Residues in contact with LEU 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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103B ARG* 3.0 40.8 + - + +
104B ASP* 4.0 9.4 - - - +
106B PHE* 1.3 79.8 - - + +
108B ILE* 1.3 61.9 + - + +
111B SER* 3.4 20.3 + - - -
112B PRO* 4.2 14.8 - - + +
115B PRO* 3.3 41.0 - - + +
116B GLU* 3.4 23.1 - - - +
118B PHE* 4.5 1.8 - - + -
120B PHE* 3.8 20.9 - - + -
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Residues in contact with ILE 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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892A GLU* 3.9 10.6 - - + +
895A GLN* 3.7 21.1 + - - +
934A ARG* 3.4 46.2 - - - +
938A ARG* 5.7 0.4 - - - +
104B ASP* 3.2 21.3 + - + +
105B GLU* 3.1 10.2 + - - +
106B PHE 3.0 1.4 - - - -
107B LEU* 1.3 81.7 - - + +
109B GLN* 1.3 77.8 + - - +
111B SER* 4.5 2.2 + - - -
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Residues in contact with GLN 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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889A PHE* 6.1 0.7 - - - -
890A ILE* 5.2 8.5 - - - +
892A GLU* 3.6 21.6 + - - +
931A ARG* 5.2 4.6 + - - +
934A ARG* 3.8 0.2 - - - +
75B VAL* 3.7 24.7 - - + +
78B TYR* 3.7 26.7 - - + +
79B ARG* 3.2 25.3 + - - +
105B GLU* 3.0 42.8 + - + +
106B PHE 3.1 0.4 + - - -
108B ILE* 1.3 104.9 - - - +
110B ALA* 1.3 59.1 + - - +
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Residues in contact with ALA 110 (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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897A GLU* 4.9 0.9 - - - +
78B TYR* 3.7 33.4 - - + +
79B ARG* 3.5 20.9 + - - +
80B GLY 5.3 1.3 + - - +
81B ALA* 4.9 2.0 - - + +
106B PHE* 2.9 33.3 + - + +
109B GLN* 1.3 74.8 - - - +
111B SER* 1.3 72.8 + - - +
112B PRO* 3.6 6.4 - - + +
118B PHE* 5.8 0.9 - - + -
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Residues in contact with SER 111 (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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895A GLN* 2.7 33.4 + - - +
897A GLU* 4.9 3.1 - - - +
79B ARG* 3.6 11.0 + - - -
107B LEU 3.4 15.9 + - - -
108B ILE* 4.5 3.2 + - - -
110B ALA* 1.3 80.6 - - - +
112B PRO* 1.3 72.9 - - - +
113B ARG 3.9 0.5 + - - -
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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
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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