Contacts of the strand formed by residues 337 - 341 (chain A) in PDB entry 3C7N
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 PHE 337 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A TYR* 4.5 4.9 - - - -
197A ARG* 3.7 39.9 - - + -
198A ILE 3.5 2.8 + - - -
199A VAL* 3.4 11.7 - - + +
200A ALA 2.9 23.9 + - - -
335A VAL* 3.5 5.3 - - - +
336A ASP* 1.3 97.1 - - + +
338A VAL* 1.3 65.3 + - - +
339A GLU* 4.1 12.3 - - - +
360A LYS* 5.9 0.2 - - - -
361A PRO 5.7 0.4 - - - -
363A SER* 4.0 17.7 - - - +
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Residues in contact with VAL 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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200A ALA* 3.3 16.4 - - + +
202A VAL* 4.4 9.9 - - + -
335A VAL* 4.3 4.5 - - + -
337A PHE* 1.3 79.5 - - - +
339A GLU* 1.3 62.2 + - - +
340A ILE* 3.8 1.1 + - + -
354A ILE* 4.9 2.2 - - + -
358A PHE* 3.9 45.1 - - + -
360A LYS* 3.9 28.9 - - + +
361A PRO 4.3 9.5 + - - +
362A LEU* 3.7 15.3 - - + +
363A SER* 2.8 29.1 + - - +
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Residues in contact with GLU 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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182A TYR* 3.7 20.5 + - + -
186A LYS* 4.8 0.9 - - - -
199A VAL* 3.8 21.1 - - + -
200A ALA 2.8 9.3 + - - -
201A PHE* 3.4 22.5 - - + +
202A VAL 3.0 23.0 + - - -
337A PHE* 4.4 6.6 - - + +
338A VAL* 1.3 75.5 - - - +
340A ILE* 1.3 64.0 + - - +
341A ILE* 3.9 1.1 + - + +
363A SER* 3.4 24.4 - - - -
364A THR* 3.7 1.6 + - - -
365A THR* 2.8 48.7 + - - +
366A LEU* 3.8 10.1 + - + +
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Residues in contact with ILE 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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202A VAL* 3.5 4.7 - - + +
338A VAL* 3.8 1.3 + - + +
339A GLU* 1.3 73.1 - - - +
341A ILE* 1.3 66.0 + - - +
345A THR* 4.0 30.5 - - + +
351A LYS* 3.8 20.9 - - + +
354A ILE* 3.6 32.8 - - + -
362A LEU* 3.7 32.3 - - + -
363A SER 3.2 7.2 + - - +
364A THR* 3.5 30.6 - - + +
366A LEU* 5.4 1.7 + - - +
368A GLN* 3.6 20.2 + - - +
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Residues in contact with ILE 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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175A VAL* 4.7 8.1 - - + -
178A ALA* 3.9 14.4 - - + -
201A PHE* 5.2 2.9 - - + -
202A VAL 2.9 20.5 + - - +
203A ASP* 3.0 44.4 - - + +
204A ILE 3.5 1.9 + - - -
339A GLU* 3.9 3.6 + - + +
340A ILE* 1.3 79.6 - - - +
342A GLY* 1.3 62.1 + - - +
345A THR* 3.4 8.0 + - - +
366A LEU* 3.9 29.8 - - + -
368A GLN* 3.6 25.8 - - + +
371A ALA* 4.8 4.0 - - + -
372A ILE* 3.5 25.6 - - + +
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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