Contacts of the strand formed by residues 106 - 113 (chain A) in PDB entry 2Q53
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 VAL 106 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A VAL* 4.7 4.9 - - + -
105A TYR* 1.3 75.2 - - - +
107A VAL* 1.3 75.4 + - - +
108A ILE* 3.7 3.1 + - + -
125A TYR* 3.4 8.8 - - - -
126A LEU* 3.0 55.6 + - + +
128A THR* 3.7 11.4 - - + -
49B PHE* 3.9 25.6 - - + -
73B GLN* 3.6 13.7 - - - +
108B ILE* 4.1 15.7 - - + -
109B GLU 4.2 10.5 - - - +
110B VAL* 4.9 0.2 - - + -
126B LEU* 4.6 1.3 - - + -
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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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95A ASP* 3.8 15.7 - - - +
100A VAL* 4.1 12.9 - - + +
106A VAL* 1.3 76.1 - - - +
108A ILE* 1.3 72.0 + - - +
123A ARG* 3.4 44.0 - - + +
124A SER 3.8 5.2 - - - +
125A TYR* 4.0 9.0 - - + -
108B ILE* 3.1 13.3 - - - +
109B GLU* 3.1 53.3 + - + +
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Residues in contact with ILE 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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49A PHE* 5.6 0.4 - - + -
71A ILE* 4.4 6.7 - - + -
106A VAL* 4.3 2.0 - - + +
107A VAL* 1.3 87.1 - - - +
109A GLU* 1.3 62.3 + - - +
110A VAL* 3.7 21.3 - - + -
123A ARG* 3.4 5.4 - - - +
124A SER* 2.9 54.0 + - - +
125A TYR* 3.4 9.0 - - - +
126A LEU* 3.5 48.0 - - + -
106B VAL* 4.1 6.7 - - + -
107B VAL 3.2 16.8 - - - +
108B ILE* 3.8 12.1 - - + +
109B GLU 5.4 0.4 - - - -
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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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108A ILE* 1.3 75.8 - - - +
110A VAL* 1.3 68.5 + - - +
111A LYS* 4.3 11.8 - - + +
121A THR* 3.8 30.2 - - + +
122A CYS 3.3 6.7 - - - +
123A ARG* 4.7 0.4 - - - +
91B LEU* 5.8 1.2 - - - +
95B ASP* 4.1 3.6 - - - +
106B VAL* 4.7 4.3 - - - +
107B VAL* 3.3 38.2 + - + +
123B ARG* 2.8 43.3 + - - -
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Residues in contact with VAL 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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20A PHE* 3.9 21.3 - - + -
46A LEU* 4.4 20.4 - - + -
49A PHE* 5.3 7.0 - - + -
108A ILE* 3.7 27.6 - - + -
109A GLU* 1.3 80.8 - - - +
111A LYS* 1.3 64.5 + - - +
112A VAL* 4.1 10.3 - - + -
120A ILE 3.7 0.2 - - - +
121A THR* 3.3 4.7 - - - +
122A CYS* 2.7 62.8 + - + +
124A SER* 4.1 9.0 - - - -
106B VAL* 5.6 0.4 - - + -
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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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45A ARG 4.8 0.2 - - - +
46A LEU* 4.2 11.4 - - - +
47A GLN 5.7 0.3 + - - -
109A GLU* 4.3 17.0 - - + +
110A VAL* 1.3 78.1 - - - +
112A VAL* 1.3 64.8 + - - +
119A GLU* 3.7 29.9 + - + +
120A ILE 3.3 6.3 - - - +
121A THR* 4.1 21.3 - - + +
92B ASN* 4.3 16.4 + - - -
95B ASP* 4.4 15.6 + - - +
100B VAL* 6.4 1.3 - - + -
101B LYS* 4.8 15.1 - - - +
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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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20A PHE* 3.8 37.5 - - + -
44A ALA* 3.5 22.4 - - + -
45A ARG 3.3 19.1 - - - +
46A LEU* 3.9 13.5 - - + -
83A VAL* 4.3 2.9 - - + -
110A VAL* 4.1 5.4 - - + -
111A LYS* 1.3 75.6 - - - +
113A ALA* 1.3 58.2 + - - +
119A GLU* 3.1 6.3 - - - +
120A ILE* 2.5 50.7 + - + +
122A CYS* 4.0 20.0 - - - -
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Residues in contact with ALA 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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44A ALA* 3.7 5.6 - - - -
45A ARG* 3.0 29.5 + - + +
80A TRP* 4.9 0.3 - - - -
112A VAL* 1.3 79.3 - - - +
114A THR* 1.3 70.4 + - - +
117A GLY* 4.3 5.8 - - - +
118A LYS 2.9 25.1 - - - +
119A GLU* 3.7 7.6 - - + +
120A ILE* 4.5 0.7 - - - +
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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