Contacts of the strand formed by residues 351 - 358 (chain A) in PDB entry 4EVI
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 ASP 351 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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349A PHE* 3.8 0.8 - - - +
350A LYS* 1.3 82.5 - - + +
352A TYR* 1.3 85.4 + - - +
366A VAL* 3.6 6.2 - - - +
367A TYR* 2.9 46.8 + - + +
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Residues in contact with TYR 352 (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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337A GLU* 2.5 38.9 + - + +
340A TRP* 6.4 0.4 - - + -
341A ALA* 3.9 25.5 - - + +
344A PHE* 3.7 25.6 - + + -
351A ASP* 1.3 91.6 + - - +
353A LYS* 1.3 65.8 + - - +
354A ILE* 3.7 26.5 - - + -
364A ILE* 4.2 10.3 - - + -
365A GLU 3.0 13.9 - - - +
366A VAL* 4.2 3.4 - - - -
367A TYR* 4.1 5.4 - - - -
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Residues in contact with LYS 353 (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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196A ASP* 5.9 5.7 + - - +
352A TYR* 1.3 76.5 - - - +
354A ILE* 1.3 67.7 + - - +
355A THR* 4.1 17.5 + - - +
363A LEU 3.5 1.2 - - - +
364A ILE* 3.4 2.9 - - - -
365A GLU* 2.8 49.9 + - - +
367A TYR* 3.9 19.7 - - + +
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Residues in contact with ILE 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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304A VAL* 4.4 16.4 - - + -
307A HIS* 3.6 34.0 + - + +
337A GLU* 3.9 23.6 - - + +
340A TRP* 6.6 0.2 - - + -
352A TYR* 3.7 28.9 - - + -
353A LYS* 1.3 81.2 - - - +
355A THR* 1.3 66.4 + - - +
356A PRO* 4.3 2.9 - - - +
362A VAL* 3.7 23.8 - - + -
363A LEU 3.3 2.5 - - - -
364A ILE* 4.2 15.7 - - + -
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Residues in contact with THR 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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193A LYS* 3.9 13.2 - - + +
194A CYS* 3.8 26.7 - - + -
353A LYS* 4.1 20.1 + - - +
354A ILE* 1.3 76.5 + - - +
356A PRO* 1.3 77.6 - - + +
357A VAL* 3.8 1.2 - - - +
362A VAL* 3.4 2.9 - - - -
363A LEU* 2.7 42.2 + - - -
365A GLU* 4.4 8.8 + - - -
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Residues in contact with PRO 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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193A LYS* 4.0 23.5 + - - +
307A HIS* 3.9 17.7 - - + +
308A GLU* 6.0 1.6 - - + +
309A SER* 3.9 27.6 - - - +
354A ILE 4.3 2.9 - - - +
355A THR* 1.3 98.8 - - + +
357A VAL* 1.3 62.2 + - - +
361A ARG 4.3 0.2 - - - +
362A VAL* 3.9 10.3 - - + -
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Residues in contact with VAL 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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186A PHE* 3.7 33.0 - - + +
189A ALA* 3.5 28.8 - - + +
190A LEU* 3.6 20.6 - - + +
193A LYS* 3.0 30.5 + - - +
194A CYS* 3.8 18.8 - - - -
356A PRO* 1.3 80.1 - - - +
358A GLY* 1.3 60.6 - - - +
361A ARG 3.2 7.5 + - - +
362A VAL 4.0 0.4 - - - -
363A LEU 3.7 21.8 - - - +
7B VAL* 4.3 4.7 - - - +
10B LEU* 4.1 4.7 - - + +
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Residues in contact with GLY 358 (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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186A PHE* 3.9 4.5 - - - -
193A LYS* 5.2 0.7 - - - -
309A SER* 6.5 1.6 - - - -
356A PRO* 5.3 0.8 - - - +
357A VAL* 1.3 80.2 - - - +
359A GLY* 1.3 68.0 + - - +
360A LEU 3.2 3.6 - - - -
361A ARG* 3.0 21.3 + - - +
10B LEU* 3.6 15.7 - - - +
11B ASP* 3.2 14.8 - - - -
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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