Contacts of the helix formed by residues 115 - 121 (chain A) in PDB entry 3C5H
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 PRO 115 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A LEU 4.5 2.0 - - - +
114A GLN* 1.3 88.5 - - + +
116A TYR* 1.3 67.5 + - - +
117A ILE* 3.3 2.9 - - + +
118A LYS* 3.0 30.0 + - + +
119A ARG* 3.0 17.7 + - - +
304A UNX 3.9 12.6 - - - -
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Residues in contact with TYR 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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19A VAL* 3.4 7.6 - - - +
20A GLY 3.0 36.7 + - - -
22A SER* 3.2 25.1 - - - +
96A GLN* 2.6 35.4 + - + +
97A THR 3.5 21.5 - - - -
98A GLU* 4.1 8.6 + - + +
114A GLN 3.6 1.2 + - - -
115A PRO* 1.3 72.9 - - - +
117A ILE* 1.3 58.5 + - - +
119A ARG* 3.5 24.8 - - - +
120A ALA* 2.6 58.4 + - + +
180A PHE* 3.6 23.8 - + + -
184A LEU* 4.1 7.2 - - + -
304A UNX 3.5 10.0 - - - -
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Residues in contact with ILE 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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115A PRO* 3.1 3.6 + - + -
116A TYR* 1.3 75.4 - - - +
118A LYS* 1.3 61.7 + - + +
121A ALA* 3.6 21.0 + - - +
180A PHE* 3.9 30.1 - - + +
183A ASN* 3.5 40.4 - - + +
184A LEU* 3.7 25.2 - - + +
187A GLN* 3.1 30.3 - - + +
304A UNX 3.5 16.4 - - - -
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Residues in contact with LYS 118 (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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114A GLN* 3.8 33.0 + - + +
115A PRO* 3.0 24.7 + - + +
117A ILE* 1.3 77.1 - - + +
119A ARG* 1.3 65.2 + - - +
121A ALA* 3.3 13.3 + - - +
122A ALA* 3.7 7.4 + - - +
187A GLN* 4.2 28.0 - - + +
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Residues in contact with ARG 119 (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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72A HIS* 3.5 25.3 + - - +
96A GLN* 3.7 15.6 + - - +
97A THR 3.0 25.3 + - - -
98A GLU* 2.8 36.2 + - - +
113A LEU* 3.8 24.3 - - - +
114A GLN* 2.9 44.0 + - + +
115A PRO* 3.0 11.4 + - - +
116A TYR* 3.5 25.1 - - + +
118A LYS* 1.3 76.2 - - - +
120A ALA* 1.3 64.1 + - - +
122A ALA* 3.2 23.1 + - - +
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Residues in contact with ALA 120 (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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17A SER* 4.2 0.2 + - - -
19A VAL* 3.6 15.6 - - + +
96A GLN* 3.9 18.8 + - + +
116A TYR* 2.6 56.1 + - + +
119A ARG* 1.3 74.9 - - - +
121A ALA* 1.3 58.0 + - - +
122A ALA 3.2 1.8 + - - +
160A PHE* 3.5 16.8 - - - -
184A LEU* 3.9 13.5 - - + -
188A LEU* 4.6 1.3 - - - -
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Residues in contact with ALA 121 (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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117A ILE 3.6 16.2 + - - +
118A LYS* 3.3 7.5 + - - +
119A ARG 3.2 1.2 - - - -
120A ALA* 1.3 76.4 - - - +
122A ALA* 1.3 65.0 + - - +
123A THR* 3.5 3.1 + - - +
160A PHE* 3.8 2.5 - - - -
187A GLN* 3.8 32.1 - - + +
188A LEU* 3.8 18.4 - - + -
191A THR* 3.4 21.2 - - + +
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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