Contacts of the helix formed by residues 108 - 119 (chain A) in PDB entry 2H6C
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 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A THR 4.5 2.9 - - - -
52A SER* 4.2 11.8 + - - -
106A TRP 4.1 2.0 + - - -
107A PHE* 1.3 74.3 - - - +
109A GLU* 1.3 54.0 + - - +
110A GLU* 3.5 8.9 + - - +
111A CYS* 2.6 35.5 + - - +
112A LEU* 2.7 38.6 + - - +
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Residues in contact with GLU 109 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A THR 4.7 1.2 + - - -
87A LEU* 3.8 19.6 - - + +
88A TYR* 3.2 29.0 + - - -
108A SER* 1.3 71.0 - - - +
110A GLU* 1.3 57.2 + - - +
112A LEU* 2.5 35.2 + - - +
113A ARG* 3.0 40.1 + - - +
124B PHE* 3.8 24.9 - - + -
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Residues in contact with GLU 110 (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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108A SER* 3.2 7.6 + - - +
109A GLU* 1.3 78.6 - - - +
111A CYS* 1.3 65.2 + - - +
113A ARG* 3.4 25.2 + - - +
114A VAL* 3.7 11.0 + - - +
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Residues in contact with CYS 111 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A MET* 3.3 43.3 - - - +
32A GLY* 4.2 1.8 - - - -
107A PHE* 3.8 20.2 - - + -
108A SER* 2.6 34.5 + - - +
110A GLU* 1.3 75.1 - - - +
112A LEU* 1.3 63.3 + - - +
113A ARG 3.2 0.7 + - - -
114A VAL* 3.2 17.6 + - - +
115A ILE* 3.3 17.1 + - - +
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Residues in contact with LEU 112 (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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25A LEU* 5.8 3.1 - - + -
53A MET* 3.9 19.7 - - + -
87A LEU* 3.9 28.0 - - + -
107A PHE* 3.9 19.7 - - + +
108A SER 2.7 21.9 + - - +
109A GLU 2.5 15.1 + - - +
111A CYS* 1.3 71.3 - - - +
113A ARG* 1.3 61.0 + - - +
115A ILE* 3.0 35.8 + - + +
116A PHE* 3.1 23.5 + - + -
126A ILE* 4.2 21.3 - - + -
124B PHE* 4.0 14.6 - - + -
127B PHE* 4.8 8.5 - - + -
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Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A GLU* 3.0 39.4 + - - +
110A GLU* 3.5 14.8 - - - +
111A CYS 3.2 0.2 - - - -
112A LEU* 1.3 77.5 - - - +
114A VAL* 1.4 62.4 + - + +
116A PHE* 3.1 18.7 + - - +
117A ARG* 3.2 34.7 + - - +
120B GLU* 3.7 38.1 + - + +
121B ASP* 3.2 28.3 + - - +
124B PHE* 3.8 30.7 - - + +
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Residues in contact with VAL 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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31A MET* 5.0 12.6 - - - -
110A GLU 3.9 12.3 - - - +
111A CYS* 3.2 9.7 + - - +
113A ARG* 1.4 72.9 - - + +
115A ILE* 1.3 68.9 + - + +
117A ARG* 2.9 33.6 + - + +
118A THR* 3.1 19.1 + - - +
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Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A LEU* 5.0 3.8 - - + -
28A TYR* 3.9 37.9 - - + -
31A MET* 4.2 20.6 - - - -
107A PHE* 3.8 28.5 - - + -
111A CYS* 3.4 18.2 - - - +
112A LEU* 3.0 31.9 + - + +
114A VAL* 1.3 78.9 - - - +
116A PHE* 1.3 61.7 + - + +
118A THR* 3.4 9.9 + - - -
119A ASP* 3.1 25.1 + - - +
122A MET* 4.2 15.7 - - + -
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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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112A LEU* 3.1 26.8 + - + -
113A ARG* 3.5 8.7 - - - +
114A VAL 3.0 1.0 - - - -
115A ILE* 1.3 84.1 - - + +
117A ARG* 1.3 59.5 + - + +
119A ASP 3.1 21.6 - - - -
120A GLU* 3.3 12.0 + - - +
122A MET* 3.9 14.6 - - + -
123A ILE* 3.6 46.1 - - + +
126A ILE* 3.4 34.5 - - + -
120B GLU* 5.8 3.6 - - + +
123B ILE* 4.0 21.3 - - + -
124B PHE* 3.8 30.7 - + - -
127B PHE* 3.8 11.4 - + - -
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Residues in contact with ARG 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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113A ARG* 3.2 30.9 + - - +
114A VAL* 2.9 25.0 + - - +
116A PHE* 1.3 77.3 - - + +
118A THR* 1.3 65.8 + - - +
119A ASP 3.0 1.1 + - - -
120A GLU* 5.9 0.3 - - - +
120B GLU* 2.8 38.9 + - - +
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Residues in contact with THR 118 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A TYR* 4.9 8.5 - - + +
31A MET* 4.9 10.5 - - + +
114A VAL* 3.1 19.2 + - - +
115A ILE* 3.5 9.0 + - - -
117A ARG* 1.3 77.6 - - - +
119A ASP* 1.3 67.8 + - + +
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Residues in contact with ASP 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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28A TYR* 2.4 30.6 + - - +
115A ILE 3.1 11.9 + - - +
116A PHE* 3.1 5.7 - - - +
117A ARG 3.0 3.4 + - - -
118A THR* 1.3 89.2 - - + +
120A GLU* 1.3 59.7 + - - +
121A ASP* 3.9 17.0 + - - +
122A MET* 2.9 45.8 - - - +
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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