Contacts of the strand formed by residues 361 - 368 (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 ILE 361 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A ASP* 3.7 26.5 - - + -
350A GLU 3.2 10.3 - - - +
351A ARG* 3.9 29.4 - - + +
358A TRP* 3.5 38.1 - - - +
359A GLY 3.4 5.4 + - - +
360A ASP* 1.3 80.8 + - - +
362A GLY* 1.3 67.9 + - - +
363A MET* 4.2 1.0 + - - -
382A THR 4.5 1.2 - - - +
383A ASN* 3.9 12.5 - - - +
384A LEU 5.0 1.4 + - - -
397A SER* 5.0 0.4 + - - -
398A PRO 5.1 3.0 + - - +
399A VAL* 4.2 6.7 - - + -
400A ASN* 3.2 41.8 + - - +
401A ILE* 4.3 7.0 - - + -
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Residues in contact with GLY 362 (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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349A ASP* 3.6 4.9 - - - -
350A GLU* 2.8 38.7 + - - +
361A ILE* 1.3 76.9 - - - +
363A MET* 1.3 64.2 + - - -
364A VAL* 3.6 7.1 + - - -
380A THR* 5.0 0.4 - - - -
382A THR 3.5 9.6 - - - -
383A ASN* 3.7 19.7 - - - +
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Residues in contact with MET 363 (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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348A ALA 3.9 2.5 - - - -
349A ASP* 4.1 15.7 - - - +
362A GLY* 1.3 73.2 - - - +
364A VAL* 1.3 60.9 + - - +
380A THR* 3.7 0.5 - - - -
381A ILE* 2.8 43.6 + - + -
382A THR* 2.9 17.1 + - - +
400A ASN* 3.9 31.4 - - + +
402A ASP 3.9 2.0 - - - -
403A MET* 3.1 53.8 - - + +
418A TYR* 3.2 41.3 - - + -
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Residues in contact with VAL 364 (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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315A PHE* 3.8 23.6 - - + -
331A TYR* 4.2 6.7 - - + -
346A ALA 3.9 0.2 - - - +
347A GLY* 3.3 0.2 - - - -
348A ALA* 3.0 40.2 + - + +
350A GLU* 3.9 41.7 - - + +
362A GLY* 4.2 2.7 - - - +
363A MET* 1.3 79.2 - - - +
365A ILE* 1.3 70.6 + - - +
378A ARG* 5.0 7.0 - - + -
379A VAL 3.3 7.4 - - - +
380A THR* 3.7 26.0 - - + +
381A ILE* 4.5 0.7 - - - +
403A MET* 3.6 2.0 - - - +
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Residues in contact with ILE 365 (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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315A PHE* 4.1 2.0 - - - -
345A ILE* 3.7 25.4 - - + -
346A ALA 3.1 6.7 - - - +
347A GLY* 3.8 11.0 - - - -
364A VAL* 1.3 81.7 - - - +
366A ARG* 1.3 63.7 + - - +
367A ARG* 3.7 24.5 - - + -
378A ARG* 3.3 5.7 - - - -
379A VAL* 2.7 58.7 + - + +
381A ILE* 3.9 19.3 - - + -
403A MET* 4.6 4.9 - - + -
405A LEU* 4.9 2.0 - - + -
530A GLY* 3.4 22.9 - - - +
533A TRP* 4.0 15.3 - - + +
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Residues in contact with ARG 366 (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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313A ASP 4.3 5.5 + - - -
314A ILE* 2.7 50.2 + - + +
315A PHE* 3.6 21.3 - - + -
345A ILE* 3.6 3.6 - - - +
346A ALA 2.9 32.6 + - - -
365A ILE* 1.3 80.0 - - - +
367A ARG* 1.3 63.6 + - - +
375A TRP* 3.0 42.9 + - + +
376A GLY 2.7 31.1 + - - +
377A ASP* 4.4 4.9 - - - +
378A ARG* 4.0 17.0 - - - +
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Residues in contact with ARG 367 (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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341A LYS* 4.8 2.4 - - - +
343A THR* 3.9 10.7 + - + +
344A LEU 3.3 3.6 - - - -
345A ILE* 4.2 9.9 - - + -
365A ILE* 3.7 16.6 - - + -
366A ARG* 1.3 73.8 - - - +
368A SER* 1.3 60.0 + - - +
369A GLU* 3.1 34.1 + - - +
375A TRP* 3.4 4.3 - - - -
376A GLY* 2.9 29.6 + - - +
377A ASP 5.0 2.2 + - - -
379A VAL* 5.2 4.9 - - + +
529A ASP* 2.7 50.5 + - - +
530A GLY 3.8 17.7 - - - -
531A LYS* 3.4 34.1 - - - +
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Residues in contact with SER 368 (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 GLY 4.5 0.2 - - - +
343A THR* 3.4 6.3 - - - +
344A LEU* 2.8 35.3 + - - +
367A ARG* 1.3 72.5 - - - +
369A GLU* 1.3 61.3 + - - +
370A ASP* 2.9 6.5 + - - -
371A ASN 4.5 2.4 + - - -
372A GLY* 2.8 28.8 + - - -
374A THR 2.9 22.4 + - - -
375A TRP* 3.5 29.4 - - - -
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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