Contacts of the helix formed by residues 105 - 113 (chain A) in PDB entry 4OGB
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 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A GLU* 3.1 33.7 - - + +
98A ASP* 4.8 12.8 + - - +
103A GLY 3.9 11.4 + - - -
104A LEU* 1.3 77.1 + - + +
106A VAL* 1.3 63.1 + - - +
108A ARG* 3.3 8.1 + - + -
109A ILE* 3.0 23.4 + - - +
327A GLN* 5.5 2.7 - - - -
328A LEU* 5.0 2.6 - - - +
513A DMS 3.2 33.5 + - + +
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Residues in contact with VAL 106 (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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104A LEU* 2.7 23.7 + - + +
105A HIS* 1.3 72.3 - - - +
107A PHE* 1.3 75.2 + - + +
109A ILE* 3.2 7.3 + - - +
110A ALA* 2.9 26.2 + - - +
117A PRO* 4.6 2.0 - - + +
121A ILE* 3.9 24.5 - - + -
163A ILE* 4.0 24.0 - - + +
166A ALA* 4.3 4.9 - - + -
167A ASP* 4.4 17.5 - - + +
170A GLN* 6.0 0.9 - - + +
328A LEU* 4.6 5.2 - - + -
332A TRP* 4.0 20.9 - - + +
513A DMS 3.6 1.4 - - - +
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Residues in contact with PHE 107 (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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106A VAL* 1.3 75.0 - - + +
108A ARG* 1.3 64.2 + - - +
110A ALA* 3.2 8.3 + - - +
111A GLU* 3.1 30.7 + - - +
163A ILE* 4.1 13.9 - - + -
328A LEU* 3.8 17.5 - - + -
331A GLN* 3.5 50.3 - - + +
332A TRP* 3.4 55.9 - + - -
335A ARG* 3.2 39.7 - - - -
513A DMS 3.2 11.0 - - + +
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Residues in contact with ARG 108 (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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91A VAL* 3.8 21.8 - - - +
95A GLU* 3.4 24.9 + - - +
105A HIS* 3.6 15.3 - - + +
107A PHE* 1.3 72.4 - - - +
109A ILE* 1.3 62.4 + - - +
111A GLU* 3.1 19.9 + - - +
112A LEU* 2.8 61.7 + - + +
513A DMS 3.0 23.3 - - + +
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Residues in contact with ILE 109 (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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92A LEU* 4.0 15.2 - - + +
95A GLU* 3.9 23.6 - - + -
96A LEU* 3.9 15.7 - - + -
104A LEU* 3.5 45.3 - - + -
105A HIS 3.0 12.3 + - - +
106A VAL* 3.2 8.5 + - - +
108A ARG* 1.3 77.2 - - - +
110A ALA* 1.3 51.1 + - - +
112A LEU* 3.8 1.1 - - - -
113A SER* 2.7 38.5 + - - -
117A PRO* 4.2 4.7 - - + -
120A VAL* 3.8 28.3 - - + -
121A ILE* 4.1 14.4 - - + -
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Residues in contact with ALA 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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106A VAL 2.9 13.9 + - - +
107A PHE* 3.2 11.2 + - - +
109A ILE* 1.3 76.0 - - - +
111A GLU* 1.3 57.8 + - + +
113A SER* 3.3 7.3 + - - -
115A ASN* 2.8 36.2 + - - +
117A PRO* 3.8 25.1 - - + +
163A ILE* 4.0 23.8 - - + -
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Residues in contact with GLU 111 (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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88A GLN* 4.6 3.5 + - - -
107A PHE* 3.1 18.7 + - - +
108A ARG* 3.1 24.4 + - - +
110A ALA* 1.3 76.9 - - + +
112A LEU* 1.3 68.9 + - + +
114A GLY* 3.2 13.7 + - - -
115A ASN 5.0 0.2 - - - +
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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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88A GLN* 2.8 49.2 + - + +
91A VAL* 3.8 34.8 - - + -
92A LEU* 4.0 26.6 - - + +
95A GLU* 3.8 15.7 - - + -
108A ARG* 2.8 52.1 + - + +
109A ILE* 4.0 3.4 - - - +
111A GLU* 1.3 77.9 - - + +
113A SER* 1.3 59.3 + - - +
114A GLY 3.2 0.2 - - - -
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Residues in contact with SER 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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88A GLN* 5.3 0.4 - - - -
92A LEU* 4.2 10.1 - - - -
109A ILE 2.7 24.0 + - - -
110A ALA 3.3 3.1 + - - -
111A GLU 3.2 0.2 - - - -
112A LEU* 1.3 78.2 - - - +
114A GLY* 1.3 59.2 + - - +
116A ARG* 3.1 51.2 + - - +
117A PRO* 3.3 2.3 - - - +
120A VAL* 4.0 20.1 - - - +
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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