Contacts of the helix formed by residues 107 - 113 (chain B) in PDB entry 3GYQ
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 ARG 107 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B ARG* 3.4 48.1 - - - +
105B PRO* 3.9 7.3 + - + +
106B ALA* 1.3 79.0 - - - +
108B PHE* 1.3 66.5 + - - +
109B GLY* 3.1 8.1 - - - +
110B ASP* 3.1 28.9 + - - +
111B ILE 3.7 1.9 + - - -
174B VAL* 3.4 17.7 - - - +
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Residues in contact with PHE 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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107B ARG* 1.3 74.0 - - - +
109B GLY* 1.3 55.7 + - - +
111B ILE* 2.9 9.3 + - + +
112B ALA* 2.8 28.8 + - - +
146B ILE* 3.9 22.4 - - + -
174B VAL* 3.9 22.2 - - + +
176B SER* 3.3 29.6 - - - -
180B GLU* 3.8 31.0 - - + -
181B ALA* 4.0 3.6 - - - -
184B PHE* 3.5 46.1 - + + -
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Residues in contact with GLY 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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107B ARG* 3.1 7.5 - - - +
108B PHE* 1.3 80.2 - - - +
110B ASP* 1.3 62.1 + - - +
112B ALA* 4.1 7.0 - - - +
113B SER* 3.2 26.3 + - - -
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Residues in contact with ASP 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ARG* 2.9 45.8 + - - -
106B ALA* 3.6 6.1 - - - +
107B ARG* 3.1 24.4 + - - +
109B GLY* 1.3 78.0 - - - +
111B ILE* 1.3 61.6 + - - +
113B SER* 3.6 6.9 + - - -
114B ARG* 3.2 29.6 - - - +
172B PRO* 3.8 19.7 - - + -
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Residues in contact with ILE 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 ARG 4.1 5.6 - - - +
108B PHE* 2.9 9.9 + - + +
110B ASP* 1.3 78.0 - - - +
112B ALA* 1.3 60.9 + - - +
113B SER 3.3 0.4 - - - -
114B ARG* 3.1 11.2 + - - +
118B VAL* 3.5 32.1 - - + -
143B SER* 3.9 6.3 - - - +
144B GLY* 4.4 4.0 - - - -
145B ILE 4.2 14.6 - - - +
146B ILE* 3.7 27.4 - - + -
172B PRO* 3.8 20.0 - - + +
174B VAL* 3.7 22.7 - - + -
184B PHE* 4.4 11.0 - - + -
212B ARG* 2.7 31.3 + - - +
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Residues in contact with ALA 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 PHE 2.8 14.6 + - - +
109B GLY* 4.1 7.9 - - - +
111B ILE* 1.3 79.3 - - - +
113B SER* 1.3 59.6 + - - +
114B ARG 3.1 7.7 + - - +
184B PHE* 4.1 20.0 - - + -
188B SER* 4.8 6.7 - - - +
212B ARG* 3.6 12.5 + - - +
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Residues in contact with SER 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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109B GLY 3.2 17.6 + - - -
110B ASP* 3.6 9.7 + - - -
112B ALA* 1.3 77.4 - - - +
114B ARG* 1.3 63.3 + - - +
115B ARG* 5.5 2.8 + - - +
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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