Contacts of the helix formed by residues 112 - 117 (chain A) in PDB entry 4GCK
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 HIS 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107A ARG* 3.3 14.5 + - + +
110A THR* 2.8 30.9 + - - +
111A GLY* 1.3 75.5 - - - +
113A ALA* 1.3 62.6 + - - +
115A MET* 3.2 22.2 + - - +
116A PHE* 4.3 0.9 - - - -
171A SER* 4.9 11.4 - - - -
174A VAL* 3.9 19.3 - - + +
175A ARG 6.1 0.2 - - - -
110B THR 2.7 26.8 + - - -
111B GLY* 3.6 24.4 - - - -
112B HIS* 3.6 25.2 - + - -
115B MET* 3.5 30.1 - - + +
122B GLN* 5.6 0.9 + - - -
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 3.9 28.3 - - + -
28A GLY 5.1 2.2 - - - +
59A PHE* 4.4 9.0 - - + -
107A ARG* 3.0 32.6 + - + +
108A ILE* 4.1 13.7 - - + -
112A HIS* 1.3 73.9 - - - +
114A LEU* 1.3 61.8 + - - +
115A MET 3.4 1.0 + - - -
116A PHE* 3.5 22.9 + - - -
117A GLU* 4.2 9.9 - - - +
115B MET* 4.9 1.6 - - - -
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Residues in contact with LEU 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A PHE* 3.9 26.9 - - + -
63A ILE* 4.6 2.9 - - + -
108A ILE* 3.8 26.0 - - + +
111A GLY* 3.5 8.5 - - - +
112A HIS 3.2 1.2 - - - -
113A ALA* 1.3 74.2 - - - +
115A MET* 1.3 63.9 + - - +
116A PHE 3.1 3.4 - - - -
117A GLU* 3.1 23.7 + - + +
118A GLN 4.9 1.1 - - - +
119A ASP* 5.7 0.2 - - - +
121A LEU* 3.9 24.0 - - + +
122A GLN* 3.7 46.9 - - + +
125A ILE* 3.8 23.1 - - + -
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Residues in contact with MET 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111A GLY 3.5 6.9 + - - +
112A HIS* 3.2 21.1 + - - +
114A LEU* 1.3 78.3 - - - +
116A PHE* 1.3 60.1 + - + +
117A GLU 3.7 2.6 + - - +
122A GLN* 6.2 3.1 - - - -
28B GLY 4.3 5.2 - - - +
29B SER* 3.4 41.7 - - - +
30B GLN* 4.7 3.3 - - - +
107B ARG* 5.4 3.1 - - - +
112B HIS* 3.8 48.7 - - + +
113B ALA* 4.5 0.9 - - - +
115B MET* 3.8 13.0 - - + -
116B PHE* 3.2 45.3 - - + -
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Residues in contact with PHE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A GLY 4.9 0.7 - - - -
29A SER 4.0 0.7 - - - -
30A GLN* 3.4 12.6 - - - -
31A ARG* 3.2 76.5 + - + +
32A ILE* 5.0 2.2 - - + +
112A HIS 4.3 2.2 - - - -
113A ALA* 3.5 17.9 - - - +
114A LEU 3.1 0.6 - - - -
115A MET* 1.3 79.6 - - - +
117A GLU* 1.3 73.8 + - - +
31B ARG* 6.1 1.1 - - - -
115B MET* 3.5 50.9 - - + -
116B PHE* 4.0 24.9 - + - -
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Residues in contact with GLU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 4.4 1.3 + - - -
32A ILE 5.3 1.6 + - - -
55A LYS* 2.7 45.9 + - - +
56A THR* 4.4 9.5 + - - -
59A PHE* 3.8 34.0 - - + -
113A ALA 4.2 12.1 - - - +
114A LEU* 3.1 17.2 + - - +
115A MET 4.4 2.6 - - - +
116A PHE* 1.3 94.6 - - - +
118A GLN* 1.3 69.0 + - - +
119A ASP* 3.4 8.3 + - - +
121A LEU* 3.6 18.2 - - + -
29Z A 6.0 0.3 - - - +
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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