Contacts of the strand formed by residues 399 - 407 (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 VAL 399 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357A ASP 4.9 1.8 - - - +
358A TRP* 4.2 17.7 - - + -
359A GLY 3.8 21.5 - - - +
361A ILE* 4.2 4.5 - - + -
384A LEU* 5.0 0.2 - - - -
397A SER 3.4 15.3 - - - +
398A PRO* 1.3 72.1 - - - +
400A ASN* 1.3 79.4 + - - +
401A ILE* 3.9 18.8 - - + -
420A MET* 3.2 7.5 - - - +
421A PHE* 2.8 49.6 + - + +
422A PRO 4.3 7.4 - - - +
424A GLY 3.9 13.7 - - - +
426A GLY* 4.5 6.1 - - - +
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Residues in contact with ASN 400 (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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361A ILE* 3.2 41.5 + - - +
363A MET* 3.9 23.3 - - + -
382A THR* 3.4 23.4 - - - +
384A LEU* 3.6 19.8 + - - +
398A PRO 4.2 1.2 + - - -
399A VAL* 1.3 72.5 + - - +
401A ILE* 1.3 62.9 + - - +
418A TYR* 3.5 21.3 - - - -
419A ASP 3.1 16.9 + - - +
420A MET* 3.5 21.4 - - - +
522A TRP* 3.7 4.4 - - - -
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Residues in contact with ILE 401 (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* 3.3 16.2 - - - +
351A ARG* 3.3 18.2 - - - +
357A ASP* 3.5 38.6 - - + +
358A TRP 4.2 0.7 - - - +
361A ILE* 4.3 3.6 - - + -
363A MET* 4.2 3.2 - - - -
399A VAL* 3.9 14.8 - - + -
400A ASN* 1.3 77.6 - - - +
402A ASP* 1.3 83.4 + - - +
419A ASP* 3.0 38.3 + - + +
421A PHE* 4.0 9.6 - - + -
1777A DAN 3.7 27.8 - - + +
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Residues in contact with ASP 402 (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* 3.5 18.5 - - - +
349A ASP* 3.0 15.8 + - - -
363A MET* 3.9 2.0 - - - +
401A ILE* 1.3 86.1 - - - +
403A MET* 1.3 59.8 + - - +
418A TYR* 3.1 17.8 - - - -
419A ASP* 3.9 4.6 - - - +
550A PHE* 5.7 0.2 - - - -
553A VAL* 3.2 26.8 - - + +
555A PRO* 4.2 9.0 - - + -
575A TYR* 4.8 2.1 + - - -
632A GLU* 4.5 3.8 - - - +
1777A DAN 2.7 55.4 + - - +
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Residues in contact with MET 403 (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* 4.3 7.4 - - - +
335A ALA* 4.1 14.6 - - + +
347A GLY* 4.1 11.2 - - - -
348A ALA 3.5 38.1 - - - +
349A ASP* 4.4 1.2 + - - +
363A MET* 3.1 36.0 - - + +
364A VAL 3.6 17.0 - - - +
365A ILE* 4.7 2.5 - - - -
381A ILE* 4.6 2.9 - - + -
402A ASP* 1.3 73.0 - - - +
404A VAL* 1.3 62.7 + - - +
405A LEU* 4.0 19.7 - - - -
416A SER* 3.5 20.0 - - - +
417A ILE 3.1 8.5 - - - +
553A VAL* 4.1 0.9 - - - -
555A PRO* 3.2 6.6 - - - +
556A GLY 3.1 20.4 + - - +
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Residues in contact with VAL 404 (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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403A MET* 1.3 76.1 - - - +
405A LEU* 1.3 66.5 + - - +
415A PHE 3.5 1.6 - - - +
416A SER* 3.4 4.2 - - - -
417A ILE* 2.8 34.0 + - + +
553A VAL* 3.6 19.5 - - + -
554A GLY 3.2 27.4 - - - +
555A PRO* 3.8 1.1 - - + -
556A GLY 3.1 6.5 - - - +
557A THR 4.1 0.4 - - - -
558A GLY* 3.3 26.9 - - - +
572A ILE* 3.8 38.8 - - + +
573A PRO* 4.3 4.3 - - + +
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Residues in contact with LEU 405 (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* 4.0 23.6 - - + +
337A LEU* 3.8 24.9 - - + -
345A ILE* 3.7 34.8 - - + +
347A GLY* 4.3 5.4 - - - +
365A ILE* 5.0 2.2 - - + -
403A MET* 4.0 10.5 - - - -
404A VAL* 1.3 74.1 - - - +
406A VAL* 1.3 61.4 + - - +
414A ILE* 4.6 4.5 - - + -
415A PHE 3.3 14.1 - - - +
416A SER* 3.9 20.0 - - - -
533A TRP* 4.3 13.2 - - + -
556A GLY 3.0 9.8 + - - +
557A THR* 3.2 10.3 - - - +
558A GLY 2.9 24.3 + - - -
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Residues in contact with VAL 406 (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* 4.0 10.5 - - + -
404A VAL 5.6 0.4 - - - +
405A LEU* 1.3 76.8 - - - +
407A GLN* 1.3 72.1 + - - +
414A ILE* 3.5 2.3 - - - +
415A PHE* 2.8 52.7 + - + +
558A GLY* 3.6 28.5 - - - +
559A ILE* 3.8 18.6 - - - +
560A VAL* 4.0 4.3 - - + -
570A ILE* 3.6 23.1 - - + -
572A ILE* 3.8 14.8 - - + -
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Residues in contact with GLN 407 (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* 3.8 16.8 - - + +
338A LYS 4.6 1.5 - - - +
339A THR* 3.4 8.3 - - - -
340A ASP* 2.9 49.9 + - - +
406A VAL* 1.3 80.5 - - - +
408A ASP* 1.3 73.8 + - - +
409A PRO* 3.4 5.2 - - + +
412A LYS* 2.8 26.6 + - - +
413A ARG 3.5 10.3 - - - +
414A ILE* 3.5 24.2 - - + +
529A ASP* 5.1 1.2 + - - +
560A VAL* 3.4 18.3 - - - +
570A ILE* 6.0 0.2 - - - -
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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