Contacts of the strand formed by residues 330 - 338 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317B SER* 4.1 2.5 - - - -
328B ILE* 3.3 9.9 - - - +
329B LYS* 1.3 80.5 - - - +
331B TYR* 1.3 71.4 + - - +
332B ARG* 3.8 4.2 - - - +
351B ARG* 2.9 45.0 + - - +
354B HIS 3.8 2.9 - - - -
355B SER* 3.3 35.1 + - - -
761B ALA 2.9 16.4 + - - -
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Residues in contact with TYR 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B PHE* 3.4 47.3 - + + +
316B GLU 3.4 34.3 - - - -
317B SER* 4.2 0.4 - - - -
324B ASN* 4.1 5.8 + - - -
326B ASP* 4.9 1.0 + - - -
328B ILE* 3.8 17.8 - - + +
330B SER* 1.3 75.5 - - - +
332B ARG* 1.3 63.4 + - - +
348B ALA* 4.1 4.3 - - + -
349B ASP 3.4 13.9 - - - -
350B GLU* 2.6 46.5 + - + +
364B VAL* 4.1 2.5 - - + -
378B ARG* 3.4 17.2 + - - -
762B TYR* 2.8 44.6 + - - +
764B LEU* 3.9 9.0 - - + -
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Residues in contact with ARG 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330B SER* 3.8 11.0 - - - +
331B TYR* 1.3 83.6 - - - +
333B ILE* 1.3 73.6 + - + +
334B PRO 3.9 0.7 - - - -
348B ALA* 3.6 4.2 - - - +
349B ASP* 2.7 34.5 + - - +
351B ARG* 3.7 32.0 - - - +
355B SER* 4.0 9.5 + - - -
357B ASP* 4.1 7.9 + - - -
706B ARG* 3.8 7.2 - - - +
737B TYR* 3.4 17.8 - - - -
753B GLU* 2.8 39.3 + - - +
761B ALA* 4.7 3.1 - - - -
762B TYR* 3.6 21.9 - - - +
764B LEU* 4.0 6.0 - - - +
1777B DAN 2.9 39.4 + - - +
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Residues in contact with ILE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332B ARG* 1.3 91.5 - - + +
334B PRO* 1.4 68.5 - - - +
335B ALA* 3.7 1.9 + - - +
347B GLY 3.6 7.5 - - - +
348B ALA* 3.7 5.4 - - - -
349B ASP* 3.6 12.6 + - - +
351B ARG* 3.5 16.2 - - - +
402B ASP* 3.4 21.3 - - - +
403B MET* 4.3 7.9 - - - +
555B PRO* 3.1 39.0 - - + -
737B TYR* 3.7 23.8 - - + -
753B GLU* 3.0 11.9 + - - -
1777B DAN 3.3 22.9 - - - +
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Residues in contact with PRO 334 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333B ILE* 1.4 91.2 - - - +
335B ALA* 1.3 60.2 + - - +
347B GLY 3.4 8.5 - - - +
556B GLY* 3.9 10.6 + - - -
682B GLN* 4.6 5.0 + - - -
737B TYR* 3.5 40.6 - - + +
738B ASN* 3.8 1.8 - - - +
739B SER* 3.7 8.6 - - - -
751B LEU* 3.6 39.5 - - + +
752B TYR* 4.2 3.4 - - - -
753B GLU* 3.7 9.9 - - + -
764B LEU* 3.8 11.4 - - + -
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334B PRO* 1.3 73.7 - - - +
336B LEU* 1.3 60.5 + - - +
345B ILE 3.5 1.4 - - - +
346B ALA* 3.4 4.3 - - - -
347B GLY 2.7 36.3 + - - +
403B MET* 4.0 21.1 - - + +
405B LEU* 3.8 20.0 - - + +
556B GLY* 3.4 25.6 - - - +
557B THR* 4.2 0.4 - - - +
739B SER* 3.7 5.6 - - - -
751B LEU* 3.6 2.9 - - - +
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Residues in contact with LEU 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B ALA* 1.3 71.7 - - - +
337B LEU* 1.3 61.8 + - - +
344B LEU* 4.1 22.2 - - + -
345B ILE 3.6 17.0 - - - +
346B ALA* 4.5 10.3 - - + -
375B TRP* 4.6 4.7 - - + -
557B THR* 2.8 17.8 + - - -
739B SER* 2.9 38.8 + - - +
741B GLN* 2.9 39.0 + - + +
749B GLY* 3.8 24.9 - - - -
750B ILE 4.0 2.0 - - - +
751B LEU* 3.8 14.8 - - + -
766B PHE* 4.2 12.1 - - + -
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Residues in contact with LEU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335B ALA 4.2 0.2 - - - -
336B LEU* 1.3 74.5 - - - +
338B LYS* 1.3 71.6 + - - +
339B THR* 3.7 6.5 + - + +
343B THR 3.4 3.8 - - - +
344B LEU* 3.5 3.9 - - - -
345B ILE* 2.8 48.3 + - + +
405B LEU* 4.1 16.2 - - + -
406B VAL* 3.9 21.8 - - - +
407B GLN* 3.9 20.6 - - + +
414B ILE* 3.8 31.4 - - + -
557B THR* 3.8 20.6 - - + -
558B GLY 5.5 0.7 - - - +
741B GLN* 3.7 6.5 - - - +
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B LEU* 1.3 78.4 - - - +
339B THR* 1.3 65.5 + - - +
342B GLY* 3.6 32.6 + - - +
343B THR 3.4 3.6 - - - +
344B LEU* 4.2 15.5 - - + -
371B ASN* 3.3 18.8 + - - -
407B GLN* 4.4 2.6 - - - +
741B GLN* 3.0 21.2 + - + +
742B GLU 3.7 18.2 - - - +
743B LEU* 2.4 37.5 + - - +
744B GLY* 5.2 0.7 - - - -
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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