Contacts of the strand formed by residues 520 - 538 (chain B) in PDB entry 2W77
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 GLN 520 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231B TYR* 4.1 10.1 + - - -
488B LYS* 3.7 5.5 - - - -
489B SER* 3.3 39.0 + - - +
491B TRP* 3.5 29.1 - - + -
518B PRO* 3.6 3.6 - - - +
519B SER* 1.3 82.5 - - - +
521B TYR* 1.3 81.1 + - - +
522B ILE* 4.1 16.7 - - + +
559B LEU* 5.1 13.9 - - + +
5C GLY 4.9 11.2 + - - +
7C SER 5.3 1.0 + - - -
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Residues in contact with TYR 521 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487B GLY 3.5 3.1 - - - -
488B LYS* 4.2 25.6 - - + -
517B THR* 5.8 0.3 - - - -
518B PRO* 3.8 41.9 + - + +
519B SER 5.4 0.4 - - - -
520B GLN* 1.3 84.4 - - - +
522B ILE* 1.3 64.4 + - - +
523B ASP* 3.8 4.6 + - + +
559B LEU* 5.8 6.6 - - - +
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Residues in contact with ILE 522 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231B TYR* 3.8 25.8 - - + +
423B TYR* 4.6 3.6 - - - +
485B TRP* 3.5 58.6 - - + +
486B GLU* 3.3 5.8 - - - +
487B GLY 2.8 40.1 + - - +
489B SER* 4.5 5.6 - - - +
520B GLN* 4.2 22.9 - - + +
521B TYR* 1.3 75.7 - - - +
523B ASP* 1.3 64.7 + - - +
524B ASP* 4.4 10.5 - - - +
559B LEU* 6.6 0.2 - - - -
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Residues in contact with ASP 523 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
484B HIS* 2.7 33.5 + - - -
485B TRP 3.6 4.3 - - - -
486B GLU* 4.3 9.6 - - + -
521B TYR* 3.8 4.5 + - + +
522B ILE* 1.3 75.9 - - - +
524B ASP* 1.3 66.4 + - - +
525B LYS* 5.1 5.1 - - - +
557B THR 4.4 0.2 - - - +
558B GLY* 3.6 16.5 - - - -
559B LEU* 4.3 1.7 + - - +
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Residues in contact with ASP 524 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B SER 4.2 0.2 - - - +
484B HIS* 3.5 4.0 - - - -
485B TRP* 2.9 63.3 + - + +
522B ILE* 4.4 11.3 - - + +
523B ASP* 1.3 79.4 + - - +
525B LYS* 1.3 63.3 + - - +
526B THR* 4.1 2.0 + - - +
556B VAL* 4.7 12.2 - - + +
557B THR 3.6 6.7 - - - -
558B GLY* 3.5 13.1 - - - -
559B LEU* 3.9 5.9 + - - +
560B ASN* 5.8 3.3 + - - -
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Residues in contact with LYS 525 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483B SER 3.4 6.5 - - - +
484B HIS* 3.9 34.1 - - + -
523B ASP* 5.1 4.9 - - - +
524B ASP* 1.3 77.0 - - - +
526B THR* 1.3 62.3 + - - +
527B ARG* 4.1 0.3 + - - +
555B ARG 3.9 0.9 - - - +
556B VAL* 3.2 5.6 - - - -
557B THR* 2.9 47.3 + - - +
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Residues in contact with THR 526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B THR* 5.6 10.7 + - + -
481B SER 3.8 1.3 - - - +
482B PHE* 3.9 1.6 - - - -
483B SER* 2.9 45.1 + - - +
524B ASP* 4.1 2.8 - - - +
525B LYS* 1.3 73.7 - - - +
527B ARG* 1.3 68.8 + - - +
528B GLN* 4.9 2.9 - - + +
554B TYR* 3.6 40.7 + - + +
555B ARG 3.5 6.1 - - - +
556B VAL* 3.8 14.9 - - - +
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Residues in contact with ARG 527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B SER 3.3 5.2 - - - +
482B PHE* 3.7 39.5 - - + -
525B LYS 4.1 0.4 + - - +
526B THR* 1.3 76.3 - - - +
528B GLN* 1.3 65.2 + - - +
529B LEU* 3.9 38.0 - - + +
553B ASP* 4.8 4.0 + - - -
554B TYR* 3.4 5.4 + - - -
555B ARG* 2.6 69.2 + - + +
564B ARG* 3.5 25.8 - - - +
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Residues in contact with GLN 528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B PRO* 6.1 2.9 - - - +
225B THR* 5.8 5.7 - - - +
257B THR 4.9 3.7 + - - -
258B GLY* 3.4 11.9 - - - -
259B ALA* 3.2 31.3 + - - +
479B SER* 3.9 3.4 + - - +
480B ALA* 3.4 3.6 - - - -
481B SER* 2.9 45.4 + - - -
526B THR* 4.9 2.9 - - + +
527B ARG* 1.3 76.1 - - - +
529B LEU* 1.3 75.5 + - - +
550B ARG* 4.6 5.0 + - - -
552B VAL* 4.0 9.2 - - - +
553B ASP 3.2 10.1 - - - +
554B TYR* 3.9 27.5 - - + -
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Residues in contact with LEU 529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B SER* 3.3 4.7 - - - +
480B ALA* 3.7 23.1 - - + -
481B SER 4.7 0.4 - - - +
482B PHE* 5.1 5.2 - - + -
527B ARG* 3.9 36.8 - - + +
528B GLN* 1.3 94.7 - - - +
530B GLY* 1.3 58.9 + - - +
551B VAL 4.5 0.7 - - - -
552B VAL* 3.7 4.5 - - - +
553B ASP* 3.0 46.2 + - + +
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Residues in contact with GLY 530 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B THR* 2.8 11.8 + - - -
479B SER* 2.7 38.6 + - - -
529B LEU* 1.3 75.3 - - - +
531B SER* 1.3 62.2 + - - -
532B TYR* 4.3 2.0 - - - -
550B ARG* 3.7 26.0 - - - -
551B VAL 3.5 6.7 - - - -
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Residues in contact with SER 531 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
477B GLY 3.4 6.5 - - - -
478B THR* 3.0 19.9 + - - -
530B GLY* 1.3 70.6 + - - -
532B TYR* 1.3 61.6 + - - +
533B MET* 5.1 8.4 - - - +
549B GLY 3.7 0.7 - - - +
550B ARG* 3.1 4.5 - - - +
551B VAL* 2.8 49.6 + - - +
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Residues in contact with TYR 532 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B THR 5.4 1.6 - - - -
157B ARG* 3.6 15.9 + - - -
255B LEU* 4.3 14.4 - - + +
256B LEU* 4.1 20.2 - - + -
458B ASP* 2.8 35.3 + - - -
459B ILE 4.0 1.4 + - - -
460B TYR* 3.9 8.2 - - + +
475B VAL* 4.6 18.8 - - + -
476B VAL* 3.4 4.0 - - - +
477B GLY* 3.0 55.0 + - - +
478B THR* 4.2 6.1 - - - -
530B GLY 4.6 0.2 - - - -
531B SER* 1.3 80.1 - - - +
533B MET* 1.3 64.0 + - - +
534B THR* 5.3 3.8 - - - -
549B GLY 3.1 12.6 - - - +
550B ARG* 3.6 34.8 - - + -
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Residues in contact with MET 533 (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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474B LEU* 5.0 7.2 - - + -
475B VAL 3.3 6.5 - - - +
476B VAL* 4.4 18.2 - - + -
531B SER* 5.1 6.7 - - - +
532B TYR* 1.3 80.6 - - - +
534B THR* 1.3 63.0 + - - +
548B GLY* 3.1 5.5 - - - -
549B GLY* 2.9 46.2 + - - +
551B VAL* 5.4 9.2 - - + -
569B PHE* 4.9 12.6 - - + -
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Residues in contact with THR 534 (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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156B THR* 4.1 30.2 + - + -
158B LEU* 5.5 2.6 - - + +
255B LEU* 3.7 23.7 - - - +
473B GLU 3.9 0.2 - - - +
474B LEU* 3.4 8.5 - - - +
475B VAL* 2.8 49.2 + - + +
532B TYR* 5.2 3.9 - - - +
533B MET* 1.3 78.0 + - - +
535B ALA* 1.3 72.7 + - - +
536B ARG 4.3 0.4 + - - +
546B PHE* 4.8 5.2 - - + -
547B LEU 3.7 10.1 - - - +
548B GLY* 4.1 4.4 - - - -
572B TYR* 4.8 7.2 - - + -
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Residues in contact with ALA 535 (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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465B PHE* 5.0 6.1 - - + -
473B GLU 3.4 8.3 - - - +
474B LEU* 4.1 13.0 - - + -
534B THR* 1.3 81.6 - - - +
536B ARG* 1.3 59.0 + - - +
537B PHE* 3.5 31.8 - - + -
545B LEU 3.5 1.6 - - - +
546B PHE* 3.3 4.9 - - - -
547B LEU 2.9 35.8 + - - +
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Residues in contact with ARG 536 (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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158B LEU* 3.7 20.9 - - + +
160B LEU* 3.9 22.4 - - - +
164B GLU* 3.8 31.1 + - - +
472B HIS* 3.6 3.4 - - - +
473B GLU* 3.0 50.5 + - + +
534B THR 4.2 0.2 - - - -
535B ALA* 1.3 69.9 - - - +
537B PHE* 1.3 61.4 + - - +
538B ASN 3.7 0.3 + - - -
544B ASN* 3.1 44.1 + - + +
545B LEU 3.7 3.1 - - - +
546B PHE* 3.3 39.8 - - + -
576B VAL* 5.7 1.6 - - - +
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Residues in contact with PHE 537 (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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465B PHE* 4.5 17.0 - + - -
467B PHE* 4.6 20.6 - + - -
472B HIS* 3.9 20.6 - + + -
535B ALA* 3.5 27.8 - - + -
536B ARG* 1.3 72.3 - - - +
538B ASN* 1.3 59.9 + - - +
539B VAL* 3.4 16.9 + - + -
544B ASN* 3.2 11.9 - - - +
545B LEU* 2.9 45.4 + - + +
547B LEU* 4.6 24.7 - - + -
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Residues in contact with ASN 538 (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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470B ARG* 2.8 61.3 + - + +
471B GLU 3.4 26.2 + - - +
472B HIS* 2.9 21.7 + - + +
536B ARG 3.7 1.8 + - - +
537B PHE* 1.3 69.8 - - - +
539B VAL* 1.3 53.2 + - - +
540B THR 3.2 17.4 + - - -
541B ASP* 5.0 2.4 - - - +
543B LEU 4.2 0.2 - - - -
544B ASN* 3.6 20.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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