Contacts of the strand formed by residues 353 - 357 (chain A) in PDB entry 3V4P
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 353 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278A CYS* 4.9 0.7 - - - -
280A VAL* 3.7 39.3 - - + -
282A LEU* 4.0 8.7 - - + -
291A LEU* 3.6 23.1 - - + -
339A ILE* 4.4 2.9 - - + -
340A VAL 3.3 13.5 - - - +
341A ASN* 4.0 4.3 - - - +
342A LEU* 3.9 4.8 - - - +
352A ASP* 1.3 79.3 - - - +
354A ALA* 1.3 61.6 - - - +
355A ILE* 4.3 17.7 - - + -
369A ILE* 3.8 2.3 - - - +
370A TYR* 3.0 45.0 + - + +
377A ILE* 5.6 2.9 - - + -
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Residues in contact with ALA 354 (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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339A ILE* 3.4 3.8 - - - +
340A VAL* 2.9 51.8 + - + +
342A LEU* 3.7 18.8 - - + +
353A VAL* 1.3 74.1 - - - +
355A ILE* 1.3 63.2 + - - +
367A ILE* 5.2 4.7 - - + -
368A TYR 3.4 8.7 - - - +
369A ILE* 4.7 9.2 - - + -
401A ILE* 3.9 13.2 - - + +
415A VAL* 5.5 1.1 - - + -
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Residues in contact with ILE 355 (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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291A LEU* 5.4 0.2 - - + -
306A VAL* 3.9 14.1 - - + -
325A LEU* 3.8 24.5 - - + -
335A PHE* 3.5 34.8 - - + -
336A GLY* 3.5 28.9 - - - +
338A SER 3.3 10.8 - - - +
339A ILE* 4.1 13.5 - - + -
353A VAL* 4.3 11.4 - - + -
354A ALA* 1.3 79.4 - - - +
356A GLY* 1.3 61.8 + - - +
367A ILE* 3.3 5.0 - - - +
368A TYR* 2.9 35.9 + - + +
370A TYR* 4.0 11.0 - - + -
401A ILE* 3.8 4.0 - - - -
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Residues in contact with GLY 356 (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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335A PHE* 3.6 0.8 - - - -
336A GLY 2.9 26.3 + - - -
337A GLU 3.3 7.3 + - - -
338A SER* 2.9 18.8 + - - -
355A ILE* 1.3 74.3 - - - +
357A ALA* 1.3 59.0 + - - +
358A PRO* 3.6 6.3 - - - -
366A ALA 4.0 3.4 - - - -
367A ILE* 4.4 1.8 - - - -
398A GLY 3.4 21.1 - - - -
401A ILE* 3.7 3.8 - - - +
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Residues in contact with ALA 357 (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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333A ALA* 3.3 16.2 - - + +
334A ARG 3.8 1.3 - - - -
335A PHE* 3.8 13.7 - - + -
356A GLY* 1.3 74.6 - - - +
358A PRO* 1.3 64.9 - - - +
359A GLN 3.1 4.4 + - - -
360A GLU* 3.2 28.2 + - - +
366A ALA 2.7 32.8 + - - +
368A TYR* 3.8 11.9 - - + -
398A GLY 4.3 0.4 + - - -
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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