Contacts of the strand formed by residues 502 - 511 (chain B) in PDB entry 3EQ6
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 GLY 502 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316B ARG* 5.3 1.1 - - - +
339B GLU* 4.9 2.9 - - - -
497B PRO* 3.6 5.5 - - - +
498B ASP 3.0 29.6 + - - +
499B PRO 4.1 2.6 + - - -
500B VAL 3.3 3.4 + - - -
501B ARG* 1.3 73.9 - - - +
503B GLU* 1.3 62.3 + - - +
568B TRP* 4.2 6.1 - - - -
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Residues in contact with GLU 503 (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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461B ARG* 6.1 0.7 - - - +
465B ILE 4.7 1.4 - - - +
466B ILE* 3.5 5.0 - - + -
467B ASN* 2.5 50.1 + - - +
468B SER* 2.9 23.4 + - - -
495B SER* 3.4 32.3 + - - -
496B SER 3.1 10.3 - - - +
498B ASP* 3.8 1.5 - - - +
501B ARG* 3.1 6.2 + - - +
502B GLY* 1.3 81.6 - - - +
504B VAL* 1.3 66.3 + - - +
568B TRP* 3.8 18.3 - - + -
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Residues in contact with VAL 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B ILE* 4.4 5.2 - - - -
468B SER* 3.8 5.2 - - - +
495B SER* 3.4 2.3 - - - -
496B SER* 2.7 45.2 + - - +
498B ASP* 3.4 32.3 - - + +
501B ARG* 3.9 18.4 - - - -
503B GLU* 1.3 76.3 - - - +
505B VAL* 1.3 64.5 + - - +
506B LYS 3.4 0.3 + - - -
542B ARG* 4.1 20.4 - - + -
543B LYS* 3.9 36.8 - - + -
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Residues in contact with VAL 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466B ILE* 4.1 12.3 - - + +
468B SER* 4.5 3.7 + - - +
473B ILE* 3.6 39.5 - - + -
478B VAL* 4.2 4.7 - - + -
493B VAL* 3.5 24.0 - - + -
494B ILE 3.8 4.5 - - - -
504B VAL* 1.3 71.4 - - - +
506B LYS* 1.3 60.4 + - - +
538B TYR 5.2 0.7 - - - +
539B LYS 3.6 18.6 - - - +
540B TYR 3.6 10.5 + - - +
541B PRO* 3.3 19.5 - - + +
542B ARG* 3.0 25.8 + - - +
543B LYS 3.5 3.6 + - - -
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Residues in contact with LYS 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492B ALA 4.0 0.5 - - - +
493B VAL* 3.3 6.2 - - - +
494B ILE* 2.8 45.4 + - + +
496B SER* 3.9 13.0 - - - -
504B VAL 3.4 0.6 + - - -
505B VAL* 1.3 74.5 - - - +
507B ALA* 1.3 64.0 + - - +
508B PHE* 3.6 22.2 - - + -
543B LYS* 3.4 28.3 - - + +
544B ILE 4.9 0.4 - - - -
545B GLU* 2.9 42.4 + - - +
567B GLU* 2.5 44.4 + - - +
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Residues in contact with ALA 507 (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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482B LEU* 3.4 32.5 - - + -
491B THR* 4.1 2.9 - - - +
492B ALA 3.7 3.4 - - - -
493B VAL* 3.9 6.5 - - + -
506B LYS* 1.3 75.4 - - - +
508B PHE* 1.3 57.3 + - - +
509B VAL* 3.9 4.7 - - + -
541B PRO* 3.8 15.4 - - + +
543B LYS 3.0 9.0 + - - +
544B ILE* 3.1 10.8 - - + +
545B GLU 2.7 32.7 + - - +
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Residues in contact with PHE 508 (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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491B THR* 2.5 27.3 + - - -
492B ALA 2.9 29.9 + - - +
494B ILE* 3.5 35.4 - - + -
506B LYS* 3.6 18.6 - - - -
507B ALA* 1.3 74.3 - - - +
509B VAL* 1.3 55.7 + - - +
545B GLU* 3.2 32.8 - - + +
547B VAL* 4.0 20.9 - - + -
550B LEU* 3.8 20.6 - - + -
563B LEU* 3.9 37.5 - - + -
567B GLU* 3.9 9.6 - - + -
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Residues in contact with VAL 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B LEU* 4.6 5.6 - - + -
488B VAL* 3.8 26.0 - - + -
490B GLU 3.6 3.1 - - - +
491B THR* 3.7 13.7 - - - +
507B ALA* 4.3 8.3 - - + -
508B PHE* 1.3 79.8 - - - +
510B VAL* 1.3 76.6 + - - +
511B LEU* 3.8 7.2 + - + -
527B LEU* 4.6 6.1 - - + -
544B ILE* 4.1 17.3 - - + -
545B GLU 2.8 6.8 + - - +
546B PHE* 3.2 30.5 - - + +
547B VAL* 2.9 23.7 + - - +
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Residues in contact with VAL 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
489B VAL* 3.0 48.5 + - + -
490B GLU* 2.8 36.9 + - + +
509B VAL* 1.3 77.7 - - - +
511B LEU* 1.3 64.9 + - - +
547B VAL* 3.5 27.1 - - + +
548B LEU* 4.0 24.5 - - + +
549B ASN* 4.2 0.9 - - - +
550B LEU* 4.1 10.1 - - + -
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Residues in contact with LEU 511 (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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487B ALA* 3.3 24.2 - - + +
489B VAL* 3.8 5.3 - - - +
509B VAL* 3.8 6.7 + - + -
510B VAL* 1.3 80.7 - - - +
512B ALA* 1.3 68.2 + - - +
513B SER* 3.4 4.7 + - - -
515B PHE* 4.1 10.3 - - + +
516B LEU* 4.4 25.4 - - + +
523B LEU* 3.4 31.4 - - + -
527B LEU* 5.1 0.9 - - + -
546B PHE* 3.5 49.1 - - + +
547B VAL 4.3 3.4 + - - -
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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