Contacts of the strand formed by residues 353 - 361 (chain A) in PDB entry 4Y2H
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 353 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A TYR 4.1 11.9 - - - +
160A GLY* 3.9 23.1 - - - +
162A LEU* 4.0 26.2 + - + +
163A HIS* 3.1 31.2 + - + +
165A SER* 6.1 0.2 - - - -
236A ILE* 3.8 3.4 - - + +
290A ILE* 5.1 1.6 - - + -
343A LEU* 4.1 9.9 - - + -
344A LEU 3.8 17.5 - - - +
345A PRO* 4.9 0.7 - - - -
351A ARG 3.6 1.4 + - - -
352A ARG* 1.3 73.5 - - - +
354A ARG* 1.3 76.3 - - - +
355A VAL* 4.2 14.8 - - + -
372A ALA* 3.4 3.1 - - - +
373A MET* 2.8 45.9 + - + -
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Residues in contact with ARG 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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342A THR 3.7 0.3 - - - +
343A LEU* 3.6 3.6 - - - -
344A LEU* 2.6 75.9 + - + +
345A PRO 4.7 4.0 + - - -
346A SER* 4.1 23.8 - - - +
347A ARG* 5.3 11.2 - - - +
353A LEU* 1.3 75.0 - - - +
355A VAL* 1.3 66.6 + - - +
356A LEU* 3.6 30.7 - - + +
370A ASP* 4.7 9.7 + - - +
371A PHE 3.4 12.8 - - - +
372A ALA* 5.1 4.0 - - - -
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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
----------------------------------------------------------
236A ILE* 3.6 23.8 - - + +
290A ILE* 4.9 5.2 - - + -
323A LEU* 3.8 30.7 - - + -
341A ILE* 3.9 20.4 - - + -
342A THR 3.3 3.1 - - - +
343A LEU* 3.9 21.8 - - + -
353A LEU* 4.2 6.3 - - + -
354A ARG* 1.3 78.2 - - - +
356A LEU* 1.3 68.0 + - - +
357A LEU* 4.5 1.8 - - + +
370A ASP* 3.4 3.1 - - - -
371A PHE* 2.8 47.4 + - + -
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Residues in contact with LEU 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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340A GLU* 3.8 1.4 - - - +
341A ILE* 3.4 4.9 - - - +
342A THR* 2.9 47.3 + - + +
344A LEU* 3.8 25.1 - - + -
354A ARG* 3.6 36.8 - - + +
355A VAL* 1.3 78.6 - - - +
357A LEU* 1.3 59.3 + - - +
370A ASP* 3.3 31.2 - - + +
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Residues in contact with LEU 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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193A ILE* 4.6 4.7 - - + -
275A PHE* 4.0 21.1 - - + -
288A PHE* 3.8 26.7 - - + -
323A LEU* 4.6 7.0 - - + -
325A LEU* 4.9 3.6 - - + -
340A GLU 3.5 8.1 - - - +
341A ILE* 4.4 11.0 - - + -
355A VAL* 3.9 4.7 + - + -
356A LEU* 1.3 73.8 - - - +
358A ARG* 1.3 71.9 + - - +
359A TYR* 4.0 21.8 - - + -
368A THR* 3.5 4.7 + - - -
369A LYS* 2.8 44.6 + - + +
370A ASP* 4.1 1.1 + - - +
371A PHE* 3.9 27.8 - - + -
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Residues in contact with ARG 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 ARG* 5.6 0.7 - - - +
339A GLY* 3.0 3.2 - - - -
340A GLU* 2.8 68.8 + - + +
357A LEU* 1.3 77.6 - - - +
359A TYR* 1.3 64.8 + - - +
366A GLU* 2.9 50.8 + - + +
367A LYS 3.5 6.9 - - - +
368A THR* 3.8 19.0 + - - +
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Residues in contact with TYR 359 (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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275A PHE* 4.4 2.5 - - + -
288A PHE* 4.0 22.2 - + + -
325A LEU* 3.4 43.1 - - + +
326A ASN 5.3 1.0 + - - -
338A SER 3.2 10.5 - - - +
339A GLY* 4.0 1.1 - - - -
357A LEU* 4.0 22.9 - - + -
358A ARG* 1.3 77.5 - - - +
360A LYS* 1.3 62.1 + - - +
361A VAL* 3.9 25.6 - - + -
364A GLN* 4.5 10.7 + - - -
365A GLU 4.4 0.2 - - - +
366A GLU* 3.4 5.9 - - - -
367A LYS* 2.8 80.0 + - + +
368A THR 4.4 6.5 - - - -
369A LYS* 5.1 4.9 - - + -
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Residues in contact with LYS 360 (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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336A ASP 3.9 1.0 - - - +
337A VAL* 3.5 4.3 - - - +
338A SER* 2.7 46.4 + - - +
359A TYR* 1.3 78.1 - - - +
361A VAL* 1.3 63.2 + - - +
362A GLY 3.6 17.2 + - - +
363A ASP* 3.8 11.4 + - - +
364A GLN 2.7 33.7 + - - +
365A GLU* 4.4 6.9 - - - +
366A GLU* 4.4 16.9 - - + +
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Residues in contact with VAL 361 (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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285A MET* 4.1 22.9 - - + -
325A LEU* 5.1 4.3 - - + -
329A VAL* 4.3 19.1 - - + -
330A GLN 5.1 0.9 - - - +
331A VAL* 3.7 28.7 - - + -
335A THR* 3.8 8.5 - - + -
336A ASP 3.9 1.6 - - - -
337A VAL* 4.2 9.0 - - + -
359A TYR* 3.9 26.0 - - + -
360A LYS* 1.3 73.8 - - - +
362A GLY* 1.3 70.7 + - - +
364A GLN* 3.1 33.6 + - - +
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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