Contacts of the strand formed by residues 52 - 56 (chain A) in PDB entry 1NQG
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LEU* 3.2 38.1 - - + +
47A ARG* 4.1 5.5 - - - +
49A LEU* 3.5 6.8 + - + +
50A PRO 3.0 14.1 + - - +
51A GLY* 1.3 76.1 - - - +
53A ASP* 1.3 62.2 + - - +
54A ILE* 3.6 27.3 + - + -
66A ILE* 4.7 1.6 - - + -
68A ILE* 3.8 16.6 - - + -
109A TYR* 3.6 20.6 - - + +
127A VAL* 6.4 0.7 - - + -
502A GLN* 3.0 19.4 + - - +
504A LYS* 3.3 9.4 + - - +
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Residues in contact with ASP 53 (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 GLY 5.2 0.4 - - - +
52A VAL* 1.3 73.7 - - - +
54A ILE* 1.3 61.0 + - - +
67A PHE* 2.7 55.3 + - + +
70A GLY 6.2 0.4 - - - +
497A ARG 4.7 2.2 - - - -
498A ARG* 3.6 8.6 - - + +
499A ALA* 3.0 36.7 + - - +
502A GLN* 3.9 19.0 + - - +
523A LEU* 5.0 1.7 - - - +
526A ARG* 2.9 25.9 + - - -
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Residues in contact with ILE 54 (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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43A ASN* 3.7 58.8 - - + +
46A LEU* 4.0 15.3 - - + -
47A ARG* 4.3 7.3 - - + +
52A VAL* 3.6 26.5 + - + +
53A ASP* 1.3 78.5 + - - +
55A THR* 1.3 73.7 + - - +
56A GLN* 5.2 1.3 - - + -
64A SER* 4.6 1.1 - - - -
65A SER 3.1 14.8 - - - +
66A ILE* 3.9 14.4 - - + -
502A GLN* 5.7 0.2 + - - -
523A LEU* 5.9 1.0 - - - +
526A ARG* 5.3 1.0 + - - -
575A THR* 4.3 12.3 + - - +
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Residues in contact with THR 55 (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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54A ILE* 1.3 75.3 - - - +
56A GLN* 1.3 67.8 + - - +
64A SER* 3.1 20.1 - - - -
65A SER* 3.0 29.7 + - - -
67A PHE* 3.8 11.9 - - + -
497A ARG* 3.7 29.0 - - + +
526A ARG* 4.2 10.8 - - - +
575A THR* 3.6 21.1 - - - +
576A VAL* 3.2 18.0 - - + +
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Residues in contact with GLN 56 (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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41A SER* 6.3 0.4 - - - -
43A ASN* 3.4 26.4 + - - +
54A ILE* 5.2 1.6 - - + -
55A THR* 1.3 77.8 - - - +
57A ASN* 1.3 57.7 + - - +
58A GLY* 2.7 30.1 + - - +
59A GLY 3.3 24.1 + - - +
60A SER* 4.2 2.9 + - - +
61A GLY 4.1 9.1 - - - +
62A GLN 3.4 26.0 + - - +
63A LEU 3.5 4.9 - - - +
64A SER* 3.6 5.8 - - - +
97A SER* 4.2 5.9 - - - +
575A THR* 3.0 20.2 + - - +
576A VAL* 3.2 13.2 + - - +
579A TYR* 4.2 2.9 - - - +
581A THR* 5.6 1.9 - - - +
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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