Contacts of the strand formed by residues 102 - 106 (chain A) in PDB entry 2PQA
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 MET 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ILE* 3.8 26.4 - - + +
54A LEU* 3.7 35.2 - - + -
55A LEU* 4.0 20.2 - - + -
92A TYR 3.5 2.3 - - - +
93A LYS* 3.6 1.6 - - - -
94A ILE* 3.1 28.8 + - - +
100A ALA 3.5 0.8 + - - -
101A PRO* 1.3 72.4 - - - +
103A ASP* 1.3 79.8 + - - +
104A VAL* 3.6 6.5 + - + +
132A LEU* 5.0 1.3 - - + -
139A LYS* 3.7 35.4 - - + +
140A SER* 3.9 8.1 - - - -
141A LEU* 4.0 17.7 - - + +
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Residues in contact with ASP 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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91A VAL* 3.9 18.5 - - + +
92A TYR 3.5 2.9 - - - +
93A LYS* 3.6 29.0 - - - +
101A PRO 4.4 0.4 + - - -
102A MET* 1.3 78.0 - - - +
104A VAL* 1.3 59.6 + - - +
105A ARG* 4.3 11.7 + - - +
138A LYS* 2.7 31.2 + - - +
139A LYS 4.7 2.0 + - - +
140A SER* 3.3 19.2 - - - -
141A LEU 2.9 23.9 + - - -
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Residues in contact with VAL 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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51A ILE* 6.5 0.2 - - + -
76A ILE* 5.8 0.9 - - + -
90A ILE 3.5 1.0 - - - +
91A VAL* 4.7 0.6 - - - +
92A TYR* 3.0 34.7 + - + +
94A ILE* 3.9 28.7 - - + -
102A MET* 4.1 10.3 - - + +
103A ASP* 1.3 79.6 - - - +
105A ARG* 1.3 64.1 + - - +
106A GLN 3.8 0.3 + - - -
128A VAL* 4.1 13.2 - - + -
141A LEU* 3.3 30.1 - - + +
143A ALA* 3.7 27.4 - - + -
146A ILE* 4.2 11.7 - - + -
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Residues in contact with ARG 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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89A ASN* 3.5 28.5 - - - +
90A ILE 3.2 2.9 - - - +
91A VAL* 3.7 27.4 - - + +
103A ASP* 4.9 11.5 + - - +
104A VAL* 1.3 71.9 - - - +
106A GLN* 1.3 59.4 + - - +
107A TRP* 3.5 16.8 - - + -
135A PHE* 4.8 21.1 - - - -
138A LYS* 6.4 0.4 - - - +
140A SER* 2.9 34.9 + - - -
141A LEU 2.9 21.4 + - - +
142A VAL* 4.4 11.3 - - - +
143A ALA* 2.9 29.8 + - - +
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Residues in contact with GLN 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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89A ASN* 3.2 3.3 - - - +
90A ILE* 2.8 37.4 + - + +
92A TYR* 4.2 14.6 - - + +
104A VAL 3.8 0.2 + - - -
105A ARG* 1.3 72.2 - - - +
107A TRP* 1.3 87.5 + - - +
108A VAL* 4.2 13.5 + - + +
143A ALA* 3.2 22.6 - - - +
144A PHE 4.5 4.6 + - - -
145A LYS* 4.6 4.8 - - - +
146A ILE* 3.4 50.5 + - + +
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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