Contacts of the strand formed by residues 108 - 112 (chain A) in PDB entry 2J2C
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 ASN 108 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A VAL 3.5 1.2 - - - +
102A PHE* 3.5 7.0 - - - -
103A ASP* 2.8 29.7 + - + +
106A TYR* 3.4 9.6 - - - +
107A GLY* 1.3 78.3 - - - +
109A LEU* 1.3 58.5 + - - +
110A LEU* 3.8 12.5 + - + -
121A CYS* 3.8 12.0 - - - -
122A ALA 3.4 6.1 - - - +
123A HIS* 3.0 35.0 + - - +
128A ILE* 5.2 0.6 - - - +
136A GLN* 2.8 28.7 + - - +
137A TYR* 3.0 31.4 + - - +
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Residues in contact with LEU 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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95A PHE* 3.7 27.4 - - + -
100A LEU* 4.3 12.1 - - + -
101A VAL 3.4 6.3 - - - +
102A PHE* 3.8 21.3 - - + -
107A GLY 4.2 0.6 + - - -
108A ASN* 1.3 71.5 - - - +
110A LEU* 1.3 60.4 + - - +
120A VAL 3.9 0.7 - - - +
121A CYS* 3.5 4.9 + - - -
122A ALA* 2.9 35.4 + - + +
124A GLY 5.7 0.4 - - - +
153A LEU* 3.6 30.7 - - + -
162A THR* 3.4 33.0 - - + +
165A LEU* 4.8 2.5 - - + -
166A ALA* 4.2 9.6 - - + +
437A MET* 4.1 15.5 - - + +
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Residues in contact with LEU 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LEU* 3.4 9.1 - - - -
101A VAL* 2.7 48.6 + - + +
103A ASP* 4.1 12.6 - - + -
108A ASN* 3.8 6.7 - - + +
109A LEU* 1.3 78.4 - - - +
111A LYS* 1.3 60.5 + - - +
112A VAL* 4.0 14.9 + - + -
118A LEU* 4.4 9.0 - - + -
120A VAL 3.4 3.8 - - - +
121A CYS* 3.5 37.2 - - + -
137A TYR* 3.7 27.4 - - + +
142A ILE* 3.8 33.0 - - + -
150A PHE* 4.3 4.5 - - + -
437A MET* 6.0 0.2 - - - -
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Residues in contact with LYS 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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97A THR* 5.0 4.3 - - - -
99A GLY 5.7 1.1 - - - +
100A LEU* 3.6 19.7 - - + +
110A LEU* 1.3 72.1 - - - +
112A VAL* 1.3 57.8 + - - +
118A LEU* 3.9 0.3 - - - -
119A LEU* 2.7 35.2 + - + -
120A VAL* 3.0 38.8 + - + +
431A ASP* 5.1 0.6 + - - -
437A MET* 2.8 28.4 + - - +
438A GLY* 3.5 9.3 - - - -
439A SER 2.8 27.8 + - - +
440A LEU 5.1 0.2 - - - -
442A ARG 2.9 17.3 + - - -
443A SER* 4.1 11.2 - - - +
448A THR* 3.4 27.1 - - + -
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Residues in contact with VAL 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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99A GLY 5.8 2.3 + - - +
101A VAL* 4.1 18.8 - - + +
110A LEU* 4.0 17.9 + - + +
111A LYS* 1.3 80.9 - - - +
113A ASP* 1.3 70.8 + - - +
116A GLY* 4.2 9.2 - - - +
117A ASN 3.2 13.0 - - - +
118A LEU* 4.2 8.7 - - + -
119A LEU* 3.8 6.2 - - - +
142A ILE* 4.0 28.9 - - + -
144A ARG* 5.2 3.1 - - - -
448A THR* 3.4 9.7 - - - -
449A LEU* 2.9 34.4 + - + +
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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