Contacts of the helix formed by residues 102 - 111 (chain A) in PDB entry 4RG7
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 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A GLN 3.6 3.1 + - - -
101A LYS* 1.3 75.7 - - - +
103A HIS* 1.3 58.4 + - - +
104A ASP* 2.9 22.9 + - - +
105A ASP* 2.9 23.2 + - - +
106A ILE* 2.6 34.4 + - - +
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Residues in contact with HIS 103 (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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101A LYS 4.0 0.6 + - - -
102A SER* 1.3 76.3 + - - +
104A ASP* 1.3 60.0 + - - +
106A ILE* 3.6 14.5 - - - +
107A VAL* 2.9 38.0 + - + +
118A LEU* 4.7 14.6 - - + -
140A LYS* 5.0 11.9 - - + -
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Residues in contact with ASP 104 (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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102A SER* 2.9 15.2 + - - +
103A HIS* 1.3 79.6 - - - +
105A ASP* 1.3 62.8 + - - +
107A VAL* 3.7 6.2 + - - +
108A THR* 2.9 28.1 + - - -
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Residues in contact with ASP 105 (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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101A LYS* 4.1 14.9 - - + -
102A SER* 2.9 33.7 + - - +
104A ASP* 1.3 79.8 - - - +
106A ILE* 1.3 57.8 + - - +
108A THR* 3.0 9.5 + - - -
109A GLU* 2.9 30.3 + - - +
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Residues in contact with ILE 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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92A LEU 4.5 14.4 - - - +
93A SER* 5.0 2.2 - - - -
101A LYS* 4.1 19.3 - - + +
102A SER 2.6 21.4 + - - +
103A HIS* 3.6 14.1 - - - +
105A ASP* 1.3 72.7 - - - +
107A VAL* 1.3 59.5 + - - +
109A GLU* 3.3 10.1 + - - +
110A PHE* 2.9 39.4 + - + +
114A ALA* 4.8 2.0 - - + -
117A THR* 3.9 21.1 - - - +
118A LEU* 4.2 24.5 - - + -
121A LEU* 3.7 29.4 - - + -
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Residues in contact with VAL 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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103A HIS* 2.9 27.3 + - + +
104A ASP* 3.9 6.1 - - - +
106A ILE* 1.3 71.6 - - - +
108A THR* 1.3 58.2 + - - +
111A GLY* 2.5 40.2 + - - +
114A ALA* 3.7 25.1 - - + -
118A LEU* 4.5 12.8 - - + -
144A LEU* 5.7 6.3 - - + -
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Residues in contact with THR 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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104A ASP 2.9 14.0 + - - -
105A ASP* 3.0 12.8 + - - -
107A VAL* 1.3 80.4 - - - +
109A GLU* 1.3 65.4 + - - +
111A GLY* 4.1 3.3 + - - -
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Residues in contact with GLU 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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67A THR 4.4 12.6 - - - +
69A PRO* 3.5 26.8 - - + +
72A LYS* 5.2 4.3 - - - +
91A ILE 5.6 2.3 - - - +
92A LEU 4.6 8.7 - - - +
105A ASP 2.9 16.5 + - - +
106A ILE* 3.7 8.9 - - - +
108A THR* 1.3 81.3 - - - +
110A PHE* 1.3 87.0 + - + +
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Residues in contact with PHE 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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69A PRO* 3.9 31.9 - - + +
72A LYS* 4.5 11.0 - - + -
73A TYR* 5.2 1.3 - - + -
91A ILE 5.4 0.7 - - - -
92A LEU* 3.5 36.3 - - + -
106A ILE* 2.9 25.4 + - + +
109A GLU* 1.3 106.5 - - + +
111A GLY* 1.3 60.6 + - - +
112A ASP* 3.0 11.3 + - - +
113A SER* 3.2 20.2 + - - -
114A ALA* 3.5 16.2 - - - +
117A THR* 3.0 45.1 - - + -
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Residues in contact with GLY 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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107A VAL* 2.5 32.0 + - - +
108A THR 4.6 4.0 - - - -
109A GLU 3.6 0.8 - - - -
110A PHE* 1.3 69.2 - - - +
112A ASP* 1.3 59.0 + - - -
114A ALA* 3.2 21.8 - - - +
144A LEU* 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