Contacts of the helix formed by residues 108 - 122 (chain B) in PDB entry 5WRV
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 108 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B PHE* 5.4 0.2 - - - +
106B GLN* 3.9 20.1 + - + +
107B GLN* 1.3 82.7 - - - +
109B ASP* 1.3 60.3 + - - +
110B LYS* 3.5 14.8 - - + +
111B LEU* 3.2 29.0 + - + +
112B LYS* 3.0 30.2 + - - +
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Residues in contact with ASP 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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597A HIS* 5.4 2.7 - - + +
108B THR* 1.3 73.9 - - - +
110B LYS* 1.3 59.3 + - - +
112B LYS* 3.3 19.3 + - - +
113B GLU* 2.9 28.2 + - - +
135B LEU* 4.2 10.6 - - + +
138B ASN* 5.4 6.1 - - - +
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Residues in contact with LYS 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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597A HIS* 2.8 55.4 + - + -
599A ALA* 4.6 14.3 + - - +
82B PHE* 3.4 47.1 - - + -
83B GLU* 5.1 4.0 + - - +
108B THR* 3.5 13.2 - - + +
109B ASP* 1.3 75.2 - - - +
111B LEU* 1.3 67.4 + - - +
113B GLU* 3.3 2.4 + - - +
114B LEU 3.0 18.2 + - - -
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Residues in contact with LEU 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B SER* 4.3 4.7 - - - -
82B PHE* 3.8 39.3 - - + +
85B ALA* 5.2 0.2 - - + -
101B ILE* 4.0 35.8 - - + +
104B ALA* 3.8 17.0 - - + -
106B GLN 3.2 27.1 - - - +
107B GLN* 3.7 15.9 - - - +
108B THR* 3.2 26.2 + - + +
110B LYS* 1.3 77.2 - - - +
112B LYS* 1.3 58.0 + - - +
114B LEU* 3.3 4.1 + - + +
115B TYR* 2.8 29.8 + - - +
201B SO4 5.4 1.3 - - - +
205B GOL 4.7 1.1 - - - -
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Residues in contact with LYS 112 (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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108B THR 3.0 14.3 + - - +
109B ASP* 3.6 18.7 + - - +
110B LYS 3.3 0.2 - - - -
111B LEU* 1.3 73.2 - - - +
113B GLU* 1.3 66.1 + - - +
115B TYR* 3.3 2.6 + - - +
116B GLY 3.0 19.2 + - - -
131B VAL* 3.6 20.9 - - + +
134B ASP* 2.8 33.5 + - - +
135B LEU* 3.7 23.8 - - + -
138B ASN* 5.5 1.2 - - - +
205B GOL 3.8 25.3 + - - +
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Residues in contact with GLU 113 (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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593A LEU* 3.7 11.0 - - - +
594A ALA* 3.8 13.0 - - - +
597A HIS* 2.9 30.2 + - + +
109B ASP 2.9 13.6 + - - +
110B LYS 3.5 9.0 - - - +
112B LYS* 1.3 78.4 - - - +
114B LEU* 1.3 62.9 + - - +
116B GLY* 3.3 2.4 + - - -
117B GLN* 3.3 20.6 + - - +
132B TYR* 4.1 0.7 + - - -
135B LEU* 3.9 20.7 - - + +
147B ARG* 2.7 46.8 + - - +
203B NA 2.8 25.2 - - - -
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Residues in contact with LEU 114 (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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594A ALA* 4.0 14.8 - - + +
82B PHE* 3.9 14.6 - - + +
85B ALA* 3.6 20.0 - - + +
86B TYR* 3.4 43.5 - - + +
89B TYR* 3.8 37.5 - - + -
101B ILE* 3.9 10.8 - - + -
110B LYS 3.0 12.9 + - - +
111B LEU* 3.7 7.4 - - + +
113B GLU* 1.3 73.9 - - - +
115B TYR* 1.3 55.2 + - - +
117B GLN* 3.0 7.8 + - - +
118B VAL* 2.8 34.5 + - + +
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Residues in contact with TYR 115 (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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98B LEU* 3.7 28.5 - - + -
101B ILE* 3.8 27.5 - - + +
102B GLU* 4.5 9.5 + - + -
111B LEU 2.8 17.7 + - - +
112B LYS* 3.4 8.7 - - + +
114B LEU* 1.3 75.8 - - - +
116B GLY* 1.3 56.5 + - - +
118B VAL* 3.2 3.7 + - + +
119B LEU* 2.9 52.8 + - + +
124B ARG* 3.8 8.1 + - - -
127B GLU* 2.6 34.7 + - - -
131B VAL* 3.8 21.1 - - + -
205B GOL 3.7 38.9 + - - +
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Residues in contact with GLY 116 (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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112B LYS 3.0 11.1 + - - -
113B GLU 3.3 4.5 + - - -
114B LEU 3.3 0.2 - - - -
115B TYR* 1.3 75.3 - - - +
117B GLN* 1.3 55.9 + - - +
119B LEU* 3.5 3.0 + - - -
120B TYR* 3.1 22.7 + - - +
128B CYS* 3.3 14.6 - - - -
131B VAL* 3.8 23.4 - - - +
132B TYR* 3.8 19.2 - - - -
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Residues in contact with GLN 117 (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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590A PHE* 3.8 16.6 - - + -
591A PHE 4.2 0.4 - - - -
592A ASP* 2.9 26.5 - - - +
593A LEU 3.1 5.9 - - - +
594A ALA* 2.9 37.9 - - - +
89B TYR* 3.3 31.9 + - + +
113B GLU 3.3 6.3 + - - +
114B LEU* 3.0 9.4 + - + +
116B GLY* 1.3 72.6 - - - +
118B VAL* 1.3 66.4 + - - +
120B TYR* 3.4 4.5 + - - +
121B ARG* 3.1 26.5 + - - +
132B TYR* 3.4 15.0 - - - +
203B NA 2.8 19.7 - - - -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B TYR* 4.0 23.8 - - + -
94B ILE* 4.1 10.5 - - + +
97B ALA* 4.1 13.9 - - + -
98B LEU* 4.0 25.8 - - + -
101B ILE* 3.9 17.7 - - + -
114B LEU* 2.8 25.5 + - + +
115B TYR* 3.6 7.9 - - + +
117B GLN* 1.3 69.4 - - - +
119B LEU* 1.3 61.6 + - - +
121B ARG* 3.2 6.1 + - - +
122B LEU* 2.9 46.3 + - + +
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Residues in contact with LEU 119 (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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98B LEU* 4.7 3.6 - - + -
115B TYR* 2.9 55.0 + - + +
116B GLY 3.8 3.8 - - - +
118B VAL* 1.3 76.7 - - - +
120B TYR* 1.3 61.6 + - - +
122B LEU* 3.2 5.0 + - + -
123B GLU 3.0 4.0 + - - -
124B ARG* 2.9 76.8 + - + +
127B GLU* 3.7 23.8 - - + +
128B CYS* 3.7 20.6 - - + +
131B VAL* 3.9 9.4 - - + -
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Residues in contact with TYR 120 (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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588A PRO 5.5 1.6 + - - -
590A PHE* 3.5 56.5 - + + +
116B GLY 3.1 14.5 + - - +
117B GLN 3.4 8.7 - - - +
119B LEU* 1.3 76.9 - - - +
121B ARG* 1.3 72.8 + - + +
123B GLU* 3.1 16.8 + - - +
125B TYR* 3.7 28.3 + + - -
128B CYS* 3.9 8.4 - - - -
153B ALA* 4.3 13.0 + - - +
154B VAL* 3.8 31.6 - - + -
157B ALA* 4.4 6.1 - - + +
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Residues in contact with ARG 121 (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 TYR* 3.8 29.5 + - + +
92B ASN* 3.6 30.5 - - - +
94B ILE* 3.8 30.9 - - + +
117B GLN 3.1 17.3 + - - +
118B VAL 3.2 7.6 + - - +
120B TYR* 1.3 85.9 - - + +
122B LEU* 1.3 61.4 + - - +
123B GLU* 3.2 9.9 + - - +
207B GOL 3.2 34.2 + - - -
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Residues in contact with LEU 122 (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 ILE* 3.7 21.3 - - + -
95B GLU* 3.6 24.2 - - - +
98B LEU* 3.9 27.6 - - + -
118B VAL* 2.9 38.2 + - + +
119B LEU* 3.8 6.5 - - + +
120B TYR 3.2 0.4 - - - -
121B ARG* 1.3 74.9 - - - +
123B GLU* 1.3 70.3 + - - +
124B ARG* 3.1 28.2 + - - +
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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