Contacts of the strand formed by residues 337 - 341 (chain A) in PDB entry 4NSW
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 SER 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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277A SER* 3.1 30.0 + - - -
330A GLU* 3.0 26.1 + - - -
331A VAL 3.4 8.1 - - - -
332A VAL* 4.3 9.6 - - - +
335A SER 4.2 0.4 + - - -
336A LYS* 1.3 80.6 - - - +
338A CYS* 1.3 63.8 + - - +
339A LEU 5.0 0.3 + - - -
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Residues in contact with CYS 338 (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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274A LYS* 4.5 15.0 - - - -
275A ARG 4.6 6.5 - - - -
277A SER* 4.8 4.9 - - - -
288A PHE* 5.0 0.2 - - - -
297A TYR* 5.8 0.7 - - - -
308A VAL* 3.7 36.8 - - + -
330A GLU* 3.5 5.1 - - - -
331A VAL* 2.8 39.6 + - + +
336A LYS* 6.1 0.9 - - + -
337A SER* 1.3 79.2 + - - +
339A LEU* 1.3 66.7 + - - +
340A LEU* 3.6 28.4 + - + +
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Residues in contact with LEU 339 (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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274A LYS* 3.7 2.4 - - - +
275A ARG* 3.5 64.6 + - + +
277A SER* 5.4 2.4 + - - -
283A TRP* 3.7 18.4 - - + -
320A CYS* 5.6 3.8 - - - -
323A SER* 5.5 7.6 - - - +
328A CYS* 3.8 26.2 - - + -
329A PHE 4.0 8.3 - - - +
330A GLU* 4.6 14.3 - - + +
337A SER* 5.0 0.6 + - - -
338A CYS* 1.3 73.6 - - - +
340A LEU* 1.3 76.5 + - - +
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Residues in contact with LEU 340 (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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272A LEU* 3.9 14.1 - - + -
273A PHE 3.5 4.3 - - - +
274A LYS* 4.0 3.8 - - + -
283A TRP* 4.4 1.6 - - - -
288A PHE* 3.5 31.2 - - + -
295A LEU* 4.1 25.1 - - + -
328A CYS* 3.4 3.5 - - - -
329A PHE* 2.9 72.9 + - + +
331A VAL* 4.1 6.1 - - + -
338A CYS* 3.6 25.8 - - + +
339A LEU* 1.3 86.1 - - - +
341A GLN* 1.3 62.9 + - - +
351A TRP* 5.9 0.4 - - + -
355A VAL* 6.2 0.2 - - + -
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Residues in contact with GLN 341 (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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272A LEU* 3.8 7.7 - - - +
273A PHE* 2.7 51.2 + - - +
283A TRP* 3.4 38.0 - - + -
325A ARG* 3.6 7.9 - - - +
326A ARG* 3.4 25.1 + - - +
327A PHE* 3.6 3.7 - - - +
328A CYS* 4.1 4.7 - - - -
340A LEU* 1.3 76.7 - - - +
342A ALA* 1.3 72.5 + - - +
343A ASP* 5.5 0.2 - - - -
142B ALA* 2.9 45.9 + - - +
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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