Contacts of the strand formed by residues 119 - 124 (chain A) in PDB entry 3G65
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 ARG 119 (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* 5.1 5.1 + - - -
111A GLN* 4.4 16.4 - - + +
112A LEU 3.4 1.6 - - - +
113A HIS* 3.0 48.0 + - - +
114A CYS 3.0 28.1 + - - +
117A GLY* 2.9 39.9 + - - +
118A VAL* 1.3 76.2 + - - +
120A LYS* 1.3 63.2 + - - +
121A THR* 4.0 2.9 + - - +
200B HIS 3.6 1.4 - - - +
201B LEU* 3.5 5.2 - - - +
202B ASP* 3.0 45.4 + - + +
204B PRO* 5.3 1.6 - - + -
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Residues in contact with LYS 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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87A LEU* 3.4 42.4 + - + +
110A VAL 3.4 6.4 - - - +
111A GLN* 4.6 0.2 - - - -
112A LEU* 2.8 54.4 + - + +
114A CYS* 4.0 24.8 - - - -
118A VAL* 4.6 4.0 - - + -
119A ARG* 1.3 72.3 - - - +
121A THR* 1.3 60.4 + - - +
122A HIS* 3.8 9.3 - - - +
165B GLU* 4.1 31.7 + - - +
166B ALA* 5.9 0.4 - - - +
200B HIS 3.4 6.3 - - - +
201B LEU* 3.4 31.6 - - + -
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Residues in contact with THR 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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109A VAL* 3.8 20.2 - - + -
110A VAL 3.8 2.2 - - - -
111A GLN* 3.6 27.5 + - + +
119A ARG* 4.0 3.7 - - - +
120A LYS* 1.3 72.8 + - - +
122A HIS* 1.3 65.0 + - - +
123A ASN* 3.5 18.8 - - - +
198B SER 4.1 0.5 - - - +
199B SER* 3.5 4.7 - - - -
200B HIS* 3.0 45.5 + - + +
202B ASP* 5.5 2.8 + - - -
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Residues in contact with HIS 122 (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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82A SER* 5.3 3.4 - - - -
83A VAL* 3.5 30.4 - - + +
87A LEU* 3.3 32.6 - - + +
108A LEU 3.0 8.1 - - - +
109A VAL* 3.2 4.0 - - - -
110A VAL* 2.9 57.3 + - + +
112A LEU* 4.4 4.7 - - + +
120A LYS* 3.8 17.6 + - - +
121A THR* 1.3 76.2 + - - +
123A ASN* 1.3 63.8 + - - +
124A LEU* 3.7 14.9 - - + +
198B SER 4.0 1.8 - - - -
199B SER* 3.1 29.5 + - - -
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Residues in contact with ASN 123 (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 ARG* 3.6 21.6 + - + +
108A LEU 4.0 2.7 - - - -
109A VAL* 4.4 12.6 - - - +
121A THR* 3.5 20.3 - - - +
122A HIS* 1.3 74.6 - - - +
124A LEU* 1.3 64.2 + - - +
197B GLY* 3.4 7.1 - - - -
198B SER* 2.8 54.3 + - - +
200B HIS* 4.1 12.2 + - - -
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Residues in contact with LEU 124 (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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75A ILE* 4.2 19.2 - - + +
79A SER* 4.5 9.2 - - - +
80A PHE* 4.0 34.8 - - + +
82A SER* 5.9 0.2 - - - +
83A VAL* 4.1 16.6 - - + -
107A ARG* 3.5 2.8 - - - -
108A LEU* 2.8 41.5 + - - +
110A VAL* 4.3 11.9 - - + -
122A HIS* 4.3 20.9 - - + +
123A ASN* 1.3 76.2 - - - +
125A SER* 1.3 66.3 + - - +
126A PHE* 3.7 2.8 - - - -
196B ALA* 3.7 27.1 - - + +
197B GLY* 5.3 0.4 - - - -
198B SER 5.7 0.4 - - - +
199B SER* 5.3 2.9 - - - +
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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