Contacts of the helix formed by residues 102 - 113 (chain B) in PDB entry 4GUN
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 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B ASP* 2.6 25.1 + - - -
101B SER* 1.4 84.1 + - - +
103B ALA* 1.3 60.0 + - - +
104B LEU 3.7 1.0 + - - -
105B GLY 3.0 12.8 + - - -
106B LYS* 2.9 29.3 + - - +
201B GLU* 3.6 30.9 - - - +
302B SO4 3.7 25.1 - - - -
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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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102B SER* 1.3 70.5 - - - +
104B LEU* 1.4 61.9 + - - +
106B LYS* 3.8 14.2 - - - +
107B GLN* 3.2 24.1 + - - +
204B TYR* 3.7 22.9 - - + -
205B SER* 3.7 14.6 - - - +
302B SO4 2.8 21.9 + - - +
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Residues in contact with LEU 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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98B PRO* 4.4 2.5 - - + -
102B SER* 3.3 4.2 + - - +
103B ALA* 1.4 78.8 - - - +
105B GLY* 1.3 56.5 + - - +
107B GLN* 3.1 4.4 + - - +
108B ILE* 2.9 47.9 + - + +
137B ILE* 5.7 1.3 - - + -
147B LEU* 4.1 14.1 - - + -
166B ILE* 3.9 15.5 - - + -
197B TRP* 4.1 15.7 - - + -
200B ALA* 3.6 18.2 - - + -
201B GLU* 3.5 39.7 - - + +
204B TYR* 3.6 37.6 - - + +
302B SO4 5.2 0.6 + - - -
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Residues in contact with GLY 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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98B PRO* 4.8 7.4 - - - +
99B ASP 3.4 21.3 - - - -
100B THR* 3.6 11.9 - - - +
102B SER* 3.0 10.1 + - - -
104B LEU* 1.3 76.7 - - - +
106B LYS* 1.4 61.1 + - - +
108B ILE* 3.4 10.7 + - - +
109B VAL* 3.1 29.1 + - - +
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Residues in contact with LYS 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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100B THR 3.3 17.2 + - - +
101B SER* 3.3 21.6 + - - +
102B SER 2.9 17.1 + - - +
103B ALA* 3.8 11.2 - - - +
105B GLY* 1.4 74.1 - - - +
107B GLN* 1.4 56.9 - - - +
109B VAL* 3.5 6.7 + - - +
110B ALA* 3.0 29.9 + - - +
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Residues in contact with GLN 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 ALA 3.2 11.2 + - - +
104B LEU 3.1 8.4 + - - +
106B LYS* 1.4 77.8 - - - +
108B ILE* 1.3 64.2 + - - +
110B ALA* 3.5 6.5 + - - +
111B GLN* 3.0 58.4 + - - +
144B GLY 4.3 8.5 + - - +
145B GLY 3.7 11.6 + - - +
146B ALA* 4.0 5.5 - - - +
147B LEU* 3.7 13.5 - - + -
204B TYR* 3.2 27.5 + - + +
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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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98B PRO* 3.9 22.9 - - + -
104B LEU* 2.9 40.9 + - + +
105B GLY* 3.8 4.7 - - - +
107B GLN* 1.3 73.7 - - - +
109B VAL* 1.3 59.7 + - + +
112B TYR* 2.8 36.9 + - + +
113B GLY 3.3 3.2 + - - -
114B SER 3.8 7.0 - - - +
115B VAL* 3.8 35.7 - - + +
118B LEU* 3.9 24.5 - - + -
147B LEU* 3.8 18.6 - - + -
197B TRP* 4.1 7.9 - - + -
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Residues in contact with VAL 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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100B THR* 3.8 27.6 - - + +
105B GLY 3.1 15.9 + - - +
106B LYS* 3.7 7.4 - - - +
107B GLN 3.4 0.2 - - - -
108B ILE* 1.3 76.9 - - + +
110B ALA* 1.3 60.7 + - - +
113B GLY* 3.0 44.1 + - - +
114B SER* 5.4 2.7 - - - -
115B VAL* 6.5 0.9 - - + -
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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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106B LYS 3.0 19.7 + - - +
107B GLN* 3.9 9.9 - - - +
108B ILE 3.3 0.4 - - - -
109B VAL* 1.3 79.3 - - - +
111B GLN* 1.3 62.4 + - + +
144C GLY* 5.3 3.3 - - - -
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Residues in contact with GLN 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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107B GLN* 3.0 44.3 + - - +
110B ALA* 1.3 79.6 - - + +
112B TYR* 1.3 69.9 + - + +
113B GLY 3.8 0.4 - - - -
146B ALA* 4.1 4.2 - - - +
147B LEU* 2.7 49.4 + - - +
142C GLN 3.8 2.4 - - - +
143C ASN* 3.0 56.2 + - - +
144C GLY* 3.4 6.7 + - - +
146C ALA* 4.0 9.1 - - - +
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Residues in contact with TYR 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 ILE* 2.8 26.4 + - + +
111B GLN* 1.3 85.4 - - + +
113B GLY* 1.3 53.7 + - - +
114B SER 3.1 21.6 + - - +
117B ASN* 2.8 29.1 + - - +
118B LEU* 3.7 37.0 - - + +
121B ILE* 3.7 24.9 - - + -
147B LEU* 3.4 37.5 + - + +
148B ASP* 3.6 16.8 + - - -
149B VAL* 4.4 2.3 - - - +
142C GLN* 3.5 20.0 + - + -
143C ASN* 3.5 22.2 - - + +
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Residues in contact with GLY 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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108B ILE 3.3 1.0 + - - -
109B VAL* 3.0 39.6 + - - +
110B ALA 5.2 0.2 + - - -
111B GLN 3.8 0.4 - - - -
112B TYR* 1.3 74.0 - - - +
114B SER* 1.3 59.4 + - - +
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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