Contacts of the strand formed by residues 352 - 358 (chain A) in PDB entry 4Y2P
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 352 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A GLN* 4.1 4.8 + - - -
329A ALA 3.4 2.7 - - - -
331A PHE* 4.0 19.7 - - + -
344A MET* 3.8 35.9 - - + +
345A ALA* 4.7 2.0 - - + -
348A TYR 3.5 15.0 - - - +
349A PRO* 3.2 15.8 + - + +
350A GLU 3.5 0.4 - - - -
351A ARG* 1.3 78.9 - - - +
353A ARG* 1.4 66.4 + - - +
354A ALA 3.3 24.2 + - - +
355A VAL* 4.0 9.4 - - + -
486A ILE* 3.6 32.7 - - + +
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Residues in contact with ARG 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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259A PRO* 5.8 4.7 - - + -
328A GLN* 3.5 31.1 + - + +
329A ALA 2.9 18.6 + - - +
330A VAL* 3.7 21.5 - - + +
351A ARG 4.0 1.6 + - - -
352A VAL* 1.4 73.7 - - - +
354A ALA* 1.3 59.6 + - - +
487A PRO* 3.6 21.3 - - - +
545A ASP 3.1 21.4 + - - -
546A ALA* 3.1 32.3 + - - +
547A ARG 3.4 11.3 + - - +
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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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330A VAL* 3.4 13.8 - - + +
331A PHE 2.9 24.9 + - - -
352A VAL* 3.2 9.7 - - - +
353A ARG* 1.3 82.3 - - - +
355A VAL* 1.3 62.2 + - - +
486A ILE* 4.5 1.1 - - - -
487A PRO* 3.4 22.2 - - + +
541A TRP* 3.5 23.8 - - + -
545A ASP 4.6 0.7 - - - +
546A ALA* 4.4 9.6 - - + -
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Residues in contact with VAL 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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331A PHE* 3.3 3.4 - - + +
341A VAL* 3.4 45.5 - - + +
342A TRP* 3.9 25.3 - - + -
345A ALA* 3.9 19.1 - - + -
352A VAL* 4.0 10.1 - - + -
354A ALA* 1.3 79.0 - - - +
356A ALA* 1.3 64.6 + - - +
484A ILE* 4.5 1.3 - - + -
486A ILE* 4.0 7.4 - - + -
487A PRO 3.0 16.9 + - - +
488A ALA* 3.1 13.2 - - + -
489A LEU 2.9 22.2 + - - +
541A TRP* 3.3 4.3 - - - -
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Residues in contact with ALA 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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331A PHE 2.9 7.4 + - - +
332A ILE* 3.1 21.8 - - + +
333A GLY 2.8 30.7 + - - -
341A VAL* 3.5 6.4 - - - +
355A VAL* 1.3 76.5 - - - +
357A SER* 1.3 54.9 + - - +
358A LEU* 6.0 0.2 - - + -
489A LEU* 3.2 25.6 - - + +
491A VAL* 5.8 0.4 - - + -
538A LEU* 4.5 3.6 - - + -
541A TRP* 3.6 23.8 - - + -
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Residues in contact with SER 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 GLY 3.2 5.2 - - - -
338A GLY* 3.5 11.8 - - - -
341A VAL* 4.7 0.4 - - - -
342A TRP* 3.4 25.7 - - - -
356A ALA* 1.3 73.3 - - - +
358A LEU* 1.3 60.6 + - - +
359A ASN 3.9 0.4 + - - -
360A THR* 2.8 42.9 + - - -
489A LEU 3.0 6.7 + - - +
490A MET* 3.7 2.0 - - - +
491A VAL* 2.8 34.9 + - - +
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Residues in contact with LEU 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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274A TRP* 4.0 15.0 - - + -
332A ILE* 5.0 3.1 - - + -
333A GLY 2.8 14.4 + - - +
334A HIS* 3.5 7.6 - - + -
335A ASP 3.4 17.0 + - - -
356A ALA* 6.0 0.7 - - + -
357A SER* 1.3 71.9 + - - +
359A ASN* 1.3 69.6 + - - +
360A THR 2.9 15.9 + - - -
491A VAL* 3.7 34.3 - - + +
526A THR* 4.1 16.4 - - + -
527A GLN* 3.7 35.4 - - + -
534A VAL* 4.4 13.0 - - + -
538A LEU* 4.4 18.2 - - + -
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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