Contacts of the strand formed by residues 339 - 342 (chain A) in PDB entry 2G5W
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 LEU 339 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A TYR* 4.5 7.4 - - + -
18A MET* 4.1 11.4 - - - -
23A LEU* 3.6 34.5 - - + -
26A ARG* 3.8 29.2 - - - +
28A VAL* 3.9 7.4 - - + -
59A PHE* 5.5 0.2 - - + -
277A TYR* 5.2 0.7 - - + -
316A THR* 3.8 24.0 - - + -
317A PHE 3.1 5.0 + - - +
318A MET* 3.2 38.0 - - + -
319A SER 2.9 24.3 + - - -
337A ALA* 3.6 2.8 - - - +
338A ASP* 1.3 87.2 - - + +
340A VAL* 1.3 68.6 + - - +
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Residues in contact with VAL 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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12A LEU* 4.0 12.3 - - + -
26A ARG 3.2 9.2 + - - +
28A VAL* 3.0 23.0 + - - -
319A SER* 3.3 11.7 - - - +
323A PHE* 3.5 38.6 - - + -
328A GLY* 3.9 20.9 - - - +
331A ALA* 4.6 2.9 - - + -
332A VAL* 4.2 10.5 - - + -
337A ALA* 4.3 10.3 - - + -
339A LEU* 1.3 79.4 - - - +
341A SER* 1.3 59.8 + - - +
342A TYR* 3.4 27.6 - - + +
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Residues in contact with SER 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 3.2 19.7 - - - -
30A ALA* 3.8 13.4 - - - +
279A HIS* 2.8 38.3 + - - -
318A MET* 4.0 4.5 - - - +
319A SER 3.2 6.3 + - - +
320A SER* 3.0 29.1 + - - -
321A GLY 4.4 1.7 + - - -
323A PHE* 4.6 2.1 - - - -
340A VAL* 1.3 77.3 - - - +
342A TYR* 1.3 64.0 + - - +
401A FMN 4.2 4.0 + - - -
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Residues in contact with TYR 342 (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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12A LEU* 3.5 9.9 - - + +
27A VAL* 3.8 27.6 - - + -
28A VAL 2.8 11.6 + - - +
30A ALA* 3.1 20.2 + - - -
32A MET* 4.2 1.0 - - - +
323A PHE* 3.6 28.3 - - + -
324A ASN 2.7 32.8 + - - -
328A GLY* 3.4 18.7 - - - -
340A VAL* 3.4 35.1 - - + +
341A SER* 1.3 74.4 - - - +
343A GLY* 1.3 60.3 + - - +
345A LEU* 4.3 9.2 - - + -
346A PHE* 3.6 18.0 - - + +
352A LEU* 4.0 18.8 - - + -
356A PHE* 3.8 18.6 - + - -
401A FMN 3.6 3.6 - - - +
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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