Contacts of the strand formed by residues 59 - 64 (chain A) in PDB entry 1NW6
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 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A LEU* 4.4 7.0 - - + -
57A ASP 3.6 0.2 - - - -
58A SER* 1.3 93.3 - - - +
60A GLN* 1.3 62.3 + - - +
61A LEU 3.5 24.7 - - - +
62A ILE* 4.0 10.3 - - + -
95A VAL* 2.9 19.3 + - + +
96A LEU* 3.3 5.9 - - + +
97A SER* 2.8 31.0 + - - -
245A THR* 3.7 12.1 - - + +
247A LEU* 3.7 33.4 - - + +
268A ILE* 5.6 0.4 - - + -
312A LEU* 4.2 12.6 - - + -
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Residues in contact with GLN 60 (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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58A SER 4.4 0.4 + - - -
59A VAL* 1.3 75.0 - - - +
61A LEU* 1.3 61.1 + - - +
96A LEU* 4.1 1.6 - - - -
97A SER* 3.5 6.4 + - - +
99A THR* 3.0 44.1 + - - +
100A GLY* 3.0 6.0 - - - -
101A SER* 3.0 25.3 + - - +
169A PHE* 3.6 11.9 + - - +
239A LEU 3.0 20.8 + - - -
240A SER* 3.8 12.5 - - - +
241A HIS* 3.8 18.9 + - + +
244A SER* 3.6 34.1 - - - +
245A THR 3.1 10.9 + - - +
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Residues in contact with LEU 61 (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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59A VAL* 3.5 2.7 - - - +
60A GLN* 1.3 81.3 - - - +
62A ILE* 1.3 82.9 + - - +
63A ILE* 4.1 18.6 - - + -
96A LEU* 4.3 0.2 - - - -
101A SER* 3.3 17.5 - - - +
103A ALA* 4.5 3.6 - - + +
235A LEU 3.9 7.2 - - - +
236A VAL* 3.9 28.7 - - + -
239A LEU* 4.0 26.0 - - + +
240A SER* 4.0 20.6 - - - -
245A THR 3.2 3.0 + - - -
246A VAL* 3.2 18.2 - - + +
247A LEU 2.8 26.0 + - - -
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Residues in contact with ILE 62 (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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59A VAL* 4.0 8.7 - - + -
61A LEU* 1.3 82.5 - - - +
63A ILE* 1.3 73.9 + - - +
64A CYS* 4.2 2.0 - - + -
92A ALA* 3.6 38.6 - - + +
95A VAL* 3.9 12.6 - - + -
96A LEU* 3.7 18.8 - - + -
101A SER 3.1 6.7 + - - -
102A ILE* 3.4 24.6 - - + -
103A ALA* 3.0 26.5 + - - -
247A LEU* 3.2 20.4 - - + +
249A PHE* 4.0 17.5 - - + -
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Residues in contact with ILE 63 (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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61A LEU* 4.1 21.3 - - + -
62A ILE* 1.3 75.9 - - - +
64A CYS* 1.3 63.4 + - - +
65A ASP* 4.1 0.9 - - + +
103A ALA* 4.0 3.6 - - + -
105A PHE* 4.2 18.2 - - + -
227A LYS* 4.7 7.0 - - - -
232A ILE* 4.2 20.4 - - + -
235A LEU* 4.0 28.9 - - + -
236A VAL* 4.9 1.3 - - + -
246A VAL* 4.1 18.6 - - + -
247A LEU 2.9 7.6 + - - +
248A ASP* 3.4 33.5 - - + +
249A PHE* 4.5 1.9 + - - -
250A PHE 5.3 0.2 + - - -
256A THR* 3.8 26.9 - - + +
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Residues in contact with CYS 64 (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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62A ILE* 4.2 3.6 - - + -
63A ILE* 1.3 75.9 - - - +
65A ASP* 1.3 54.3 + - - +
66A PRO* 3.4 10.9 - - - +
88A TRP* 3.4 38.1 - - - -
102A ILE* 3.9 21.3 - - + -
103A ALA 2.9 16.1 + - - +
104A ILE* 3.2 8.5 - - + -
105A PHE* 2.7 33.6 + - - -
248A ASP* 5.2 0.2 - - - -
249A PHE* 4.3 5.2 - - - -
250A PHE* 4.1 14.4 - - - -
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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