Contacts of the strand formed by residues 471 - 490 (chain A) 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 GLU 471 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A PRO* 3.8 7.9 - - + +
75A GLU* 3.4 41.1 - - + +
78A ARG* 3.4 21.3 + - - -
130A THR* 2.7 32.8 + - + -
464A PRO* 3.8 24.1 - - - +
465A PHE* 3.8 9.4 + - - -
466A GLN* 3.2 27.9 + - + +
470A ARG* 1.3 73.7 - - - +
472A HIS* 1.3 58.8 + - - +
538A ASN* 3.3 18.6 + - - +
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Residues in contact with HIS 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 3.5 6.5 - - - +
464A PRO* 3.0 8.1 - - - +
465A PHE* 2.7 59.2 + + + +
467A PHE* 3.4 30.6 - + + +
468A LEU* 4.1 2.4 + - + -
470A ARG* 3.0 33.7 + - + +
471A GLU* 1.3 73.2 - - - +
473A GLU* 1.3 59.6 + - - +
536A ARG 3.2 13.9 - - - +
537A PHE* 3.4 19.1 - + + -
538A ASN 2.9 40.7 + - - -
539A VAL* 5.4 0.7 - - - -
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Residues in contact with GLU 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130A THR* 4.1 13.6 + - + +
131A MET 3.8 20.5 + - - +
132A ILE* 3.7 16.3 - - + +
158A LEU* 3.4 32.6 - - + +
159A VAL 4.6 3.7 + - - +
160A LEU* 4.2 14.0 - - - +
462A THR* 4.7 3.5 + - - -
463A GLY 3.2 16.3 - - - +
464A PRO* 3.9 0.9 - - + -
465A PHE* 3.7 7.1 - - - -
472A HIS* 1.3 74.4 - - - +
474A LEU* 1.3 61.9 + - - +
535A ALA* 3.6 2.6 - - - -
536A ARG* 2.9 55.8 + - + +
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Residues in contact with LEU 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 4.2 1.3 - - - -
410A TRP* 4.0 22.4 - - + -
461A LEU 3.8 1.0 - - - +
462A THR* 3.2 17.1 + - - -
463A GLY 2.9 20.2 + - - +
465A PHE* 4.0 19.1 - - + -
473A GLU* 1.3 74.6 - - - +
475A VAL* 1.3 66.9 + - - +
476A VAL* 5.0 6.7 - - + +
533A MET* 4.2 26.9 - - + -
534A THR 3.5 10.3 - - - +
535A ALA* 3.9 22.9 - - + -
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Residues in contact with VAL 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A THR 3.4 19.7 - - - +
157A ARG* 3.7 28.3 - - + -
158A LEU* 3.4 25.4 - - + -
460A TYR* 4.2 11.9 - - + -
461A LEU 3.3 7.0 - - - +
462A THR* 3.9 16.6 - - - +
474A LEU* 1.3 75.3 - - - +
476A VAL* 1.3 61.5 + - - +
477A GLY 4.3 0.2 - - - -
532A TYR* 4.7 8.1 - - + -
533A MET* 3.2 8.5 - - - +
534A THR* 3.0 38.1 + - - +
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Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410A TRP* 5.2 5.8 - - + -
460A TYR* 3.2 3.1 - - - +
461A LEU* 2.7 56.5 + - + +
474A LEU* 5.2 7.9 - - + -
475A VAL* 1.3 75.0 - - - +
477A GLY* 1.3 65.6 + - - +
532A TYR* 3.5 9.6 - - - +
533A MET* 4.7 23.3 - - + -
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Residues in contact with GLY 477 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459A ILE 3.0 13.9 - - - -
460A TYR* 3.8 1.6 - - - -
476A VAL* 1.3 79.8 - - - +
478A THR* 1.3 61.1 + - - -
531A SER* 3.6 2.6 - - - -
532A TYR* 2.9 54.2 + - - +
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Residues in contact with THR 478 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A LEU* 6.5 0.4 - - + -
458A ASP* 3.8 2.3 - - - +
459A ILE* 2.8 54.2 + - + +
477A GLY* 1.3 74.3 - - - -
479A SER* 1.3 63.5 + - - +
530A GLY 3.1 9.3 + - - -
531A SER* 3.1 19.2 + - - +
532A TYR* 4.2 2.0 - - - -
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Residues in contact with SER 479 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PRO* 6.0 1.6 - - - +
457A LEU 3.5 5.8 - - - -
458A ASP* 3.3 27.1 - - - -
478A THR* 1.3 79.4 + - - +
480A ALA* 1.3 64.4 + - - +
528A GLN* 5.2 3.1 + - - +
529A LEU* 3.4 4.7 - - - +
530A GLY 2.7 39.8 + - - +
532A TYR* 4.8 2.7 - - - -
550A ARG* 3.0 28.7 + - - -
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Residues in contact with ALA 480 (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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455A ASN 3.9 0.3 - - - +
456A SER* 3.4 3.6 - - - -
457A LEU* 2.9 49.7 + - + +
479A SER* 1.3 76.4 - - - +
481A SER* 1.3 61.3 + - - +
482A PHE* 4.2 14.4 - - + -
528A GLN 3.3 6.1 - - - -
529A LEU* 3.5 18.6 - - + -
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Residues in contact with SER 481 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A PRO 5.9 2.0 - - - -
225A THR* 4.7 12.6 + - - -
454A SER* 6.5 0.9 - - - -
455A ASN 3.3 4.9 - - - -
456A SER* 3.8 17.0 - - - -
480A ALA* 1.3 75.3 - - - +
482A PHE* 1.3 67.0 + - - +
483A SER* 4.2 1.1 - - - -
526A THR 4.4 0.4 - - - -
527A ARG* 3.2 6.6 - - - +
528A GLN* 2.8 61.3 + - - +
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Residues in contact with PHE 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453A LYS 4.1 0.5 - - - +
454A SER* 3.4 1.3 - - - -
455A ASN* 2.7 47.0 + - + +
480A ALA* 4.2 21.1 - - + -
481A SER* 1.3 81.2 - - - +
483A SER* 1.3 57.8 + - - +
526A THR 3.5 4.9 - - - -
527A ARG* 3.5 33.4 - - + -
529A LEU* 4.6 9.4 - - + -
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Residues in contact with SER 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A THR* 3.3 31.6 + - - +
231A TYR* 3.9 6.6 - - - -
452A THR* 4.4 7.4 - - - -
453A LYS 3.2 5.6 - - - -
454A SER* 2.9 29.2 - - - -
481A SER* 4.2 0.8 - - - -
482A PHE* 1.3 74.0 - - - +
484A HIS* 1.3 61.7 + - - +
485A TRP 4.2 0.7 - - - -
524A ASP 4.0 0.5 - - - +
525A LYS* 3.4 4.3 - - - +
526A THR* 2.9 37.3 + - - +
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Residues in contact with HIS 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A GLU 3.8 0.5 - - - +
452A THR* 3.4 4.2 - - - +
453A LYS* 2.9 37.2 + - + +
483A SER* 1.3 74.4 - - - +
485A TRP* 1.3 67.8 + - - +
486A GLU* 2.7 28.9 + - - +
523A ASP* 2.9 27.2 + - - -
524A ASP 3.3 13.5 - - - -
525A LYS* 3.6 31.0 + - + +
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Residues in contact with TRP 485 (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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228A ASN* 3.7 26.0 - - - -
230A GLY* 3.7 17.7 - - - -
231A TYR* 4.1 22.3 - + + -
423A TYR* 2.9 33.3 + + - -
451A GLU 3.6 8.3 - - - -
452A THR* 3.5 23.9 - - - +
483A SER 4.2 0.2 - - - -
484A HIS* 1.3 71.6 - - - +
486A GLU* 1.3 82.9 + - - +
487A GLY 4.6 0.2 - - - +
522A ILE* 3.5 38.8 - - + +
523A ASP* 3.4 2.4 - - - -
524A ASP* 2.8 52.2 + - + +
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Residues in contact with GLU 486 (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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450A GLY* 3.3 1.2 - - - -
451A GLU* 2.8 41.5 + - + +
453A LYS* 5.5 10.1 + - - +
484A HIS* 2.7 37.5 + - + +
485A TRP* 1.3 82.9 - - - +
487A GLY* 1.3 59.0 + - - +
522A ILE 3.8 7.0 - - - +
523A ASP* 3.6 16.8 - - - +
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Residues in contact with GLY 487 (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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423A TYR* 4.5 3.4 - - - -
449A THR 3.4 11.4 - - - -
450A GLY* 3.9 2.9 - - - -
486A GLU* 1.3 76.2 - - - +
488A LYS* 1.3 65.3 + - - +
521A TYR* 3.6 8.7 - - - -
522A ILE* 3.0 43.4 + - - +
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Residues in contact with LYS 488 (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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447A LYS 4.1 0.3 - - - +
448A TYR* 3.6 2.8 - - - +
449A THR* 3.0 45.3 + - - +
487A GLY* 1.3 77.0 - - - +
489A SER* 1.3 65.1 + - - +
490A TYR* 4.2 29.9 + - + +
518A PRO* 4.5 9.0 - - + +
520A GLN 3.5 5.8 - - - +
521A TYR* 3.9 32.3 + - + -
522A ILE* 4.4 0.8 - - - +
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Residues in contact with SER 489 (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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447A LYS 3.6 3.4 - - - -
448A TYR* 3.5 21.7 - - - -
488A LYS* 1.3 76.6 + - - +
490A TYR* 1.3 56.5 + - - +
491A TRP* 3.6 27.4 - - - -
518A PRO* 3.5 4.9 - - - +
519A SER* 2.6 32.3 + - - -
520A GLN* 3.1 29.5 + - - +
522A ILE* 4.1 9.2 - - - +
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Residues in contact with TYR 490 (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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446A GLN* 3.7 5.0 - - - +
447A LYS* 2.9 61.9 + - + +
448A TYR* 5.2 0.4 - - - -
449A THR* 5.0 7.4 - - + -
488A LYS* 4.2 30.9 + - + +
489A SER* 1.3 78.2 - - - +
491A TRP* 1.3 62.4 + - - +
492A ASN 3.9 0.4 - - - -
493A LEU* 5.1 0.9 - - - -
515A TRP* 3.6 29.9 - - + +
516A GLY 3.2 28.0 - - - -
517A THR 3.7 7.0 - - - -
518A PRO* 3.5 29.7 - - + +
519A SER* 4.0 2.5 - - - -
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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