Contacts of the strand formed by residues 330 - 338 (chain A) in PDB entry 2YA6
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 SER 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A SER* 4.1 2.7 - - - -
328A ILE* 3.3 8.7 - - - +
329A LYS* 1.3 81.5 - - - +
331A TYR* 1.3 62.5 + - - +
332A ARG* 3.7 8.3 - - - +
351A ARG* 2.8 48.0 + - - +
354A HIS 3.8 11.9 - - - -
355A SER* 3.5 18.5 + - - -
761A ALA 2.7 27.3 + - - -
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Residues in contact with TYR 331 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A PHE* 3.5 46.4 - + + +
316A GLU 3.5 35.9 - - - -
317A SER* 4.2 0.4 - - - -
324A ASN* 4.1 5.3 + - - -
326A ASP* 4.8 1.7 + - - -
328A ILE* 3.7 19.0 - - + +
330A SER* 1.3 74.5 - - - +
332A ARG* 1.3 63.1 + - - +
348A ALA* 4.3 3.4 - - + -
349A ASP 3.4 15.5 - - - +
350A GLU* 2.6 47.0 + - + -
364A VAL* 4.2 2.9 - - + -
378A ARG* 3.4 14.0 + - - -
762A TYR* 2.9 39.5 + - - +
764A LEU* 3.5 13.4 - - + +
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Residues in contact with ARG 332 (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 SER* 3.7 12.8 - - - +
331A TYR* 1.3 81.0 - - - +
333A ILE* 1.3 73.2 + - + +
334A PRO* 3.9 1.3 - - - -
348A ALA* 3.7 3.5 - - - +
349A ASP* 2.8 35.3 + - - +
351A ARG* 3.5 31.8 - - - +
355A SER* 3.7 10.9 + - - -
357A ASP* 3.8 10.3 + - - -
706A ARG* 3.9 6.6 - - - +
737A TYR* 3.5 14.3 - - - -
753A GLU* 2.9 36.4 + - - +
761A ALA* 4.1 7.0 - - - +
762A TYR* 3.6 20.0 - - + -
764A LEU* 4.2 4.7 - - - -
1777A DAN 2.9 41.6 + - - +
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Residues in contact with ILE 333 (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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332A ARG* 1.3 96.2 - - + +
334A PRO* 1.3 70.3 - - - +
335A ALA* 3.7 2.4 + - - +
347A GLY 3.7 1.1 - - - +
348A ALA* 3.6 11.4 - - - -
349A ASP* 3.5 11.9 + - - +
351A ARG* 3.4 22.4 - - - +
402A ASP* 3.5 18.2 - - - +
403A MET* 4.3 6.2 - - - +
555A PRO* 3.2 40.2 - - + -
737A TYR* 3.7 22.9 - - + -
753A GLU* 3.0 12.1 + - - -
1777A DAN 3.4 17.9 - - - +
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Residues in contact with PRO 334 (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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332A ARG 3.9 0.9 - - - -
333A ILE* 1.3 92.1 - - - +
335A ALA* 1.3 60.7 + - - +
347A GLY 3.3 7.9 - - - +
403A MET 5.8 0.2 - - - -
555A PRO 4.9 0.5 - - - -
556A GLY* 4.0 10.4 + - - -
682A GLN* 4.7 2.9 + - - -
737A TYR* 3.5 41.5 - - + +
738A ASN* 3.7 8.7 - - - +
739A SER* 3.8 8.5 - - - -
751A LEU* 3.6 33.2 - - + +
752A TYR* 4.2 3.6 - - - -
753A GLU* 3.8 9.6 - - + -
764A LEU* 3.8 11.2 - - + -
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Residues in contact with ALA 335 (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 ILE 3.7 0.2 + - - -
334A PRO* 1.3 74.9 - - - +
336A LEU* 1.3 60.8 + - - +
345A ILE 3.5 1.0 - - - +
346A ALA* 3.4 4.7 - - - -
347A GLY* 2.7 36.0 + - - +
403A MET* 4.1 19.7 - - + +
405A LEU* 4.0 21.1 - - + -
556A GLY* 3.4 24.5 - - - +
557A THR* 4.4 0.4 - - - +
739A SER* 3.7 6.3 - - - -
751A LEU* 3.6 3.0 - - - +
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Residues in contact with LEU 336 (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 ALA* 1.3 73.9 - - - +
337A LEU* 1.3 61.2 + - - +
344A LEU* 4.4 14.1 - - + -
345A ILE 3.4 13.7 - - - +
346A ALA* 4.4 3.8 - - + -
375A TRP* 4.2 22.9 - - + -
405A LEU* 4.7 0.2 - - - -
557A THR* 2.7 22.7 + - - -
739A SER* 2.9 34.4 + - - +
741A GLN* 3.0 34.1 - - + +
749A GLY* 3.8 25.4 - - - +
750A ILE 4.1 0.7 - - - +
751A LEU* 4.1 17.3 - - + +
766A PHE* 4.0 15.5 - - + -
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Residues in contact with LEU 337 (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 LEU* 1.3 74.6 - - - +
338A LYS* 1.3 72.0 + - - +
339A THR* 3.8 15.7 + - + +
343A THR 3.4 1.4 - - - +
344A LEU* 3.4 5.4 - - - -
345A ILE* 2.7 45.1 + - + +
405A LEU* 3.8 22.9 - - + -
406A VAL* 4.0 5.6 - - + -
407A GLN* 3.8 31.6 - - + +
414A ILE* 3.6 31.0 - - + -
557A THR* 3.9 19.7 - - + -
741A GLN* 3.5 4.7 - - - +
1781A FMT 5.3 4.3 - - - +
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Residues in contact with LYS 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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337A LEU* 1.3 77.0 - - - +
339A THR* 1.3 66.7 + - - +
342A GLY* 3.7 32.3 + - - +
343A THR 3.3 4.3 - - - -
344A LEU* 3.8 20.9 - - + -
371A ASN* 2.9 28.0 + - - +
407A GLN* 4.6 2.6 - - - +
741A GLN* 2.9 19.5 + - + +
742A GLU 4.1 17.7 - - - +
743A LEU* 3.1 28.5 + - + -
1781A FMT 3.9 17.7 - - - +
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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