Contacts of the strand formed by residues 621 - 634 (chain D) in PDB entry 2W3S
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 TYR 621 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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407D GLN* 5.5 0.7 - - - +
411D ASP* 3.9 10.5 - - - +
456D GLY* 3.6 3.5 - - - -
457D ILE* 3.1 51.4 + - + +
534D ASP* 2.5 31.5 + - - -
619D PHE* 3.4 3.9 - - - +
620D LEU* 1.3 97.5 - - + +
622D PHE* 1.3 80.5 + - - +
623D ALA* 4.7 1.1 - - + -
717D ASN* 3.4 25.4 - - - +
719D GLU* 4.1 8.7 - - + -
721D THR* 3.7 11.2 - - + -
726D LYS* 3.5 29.3 - - + -
727D ALA* 2.7 25.5 + - - +
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Residues in contact with PHE 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D HIS* 5.4 1.8 - - - -
403D THR* 4.3 2.5 - - + -
405D TYR* 3.2 28.0 - - - -
407D GLN* 3.8 31.2 - - + -
408D GLU 4.3 3.1 - - - -
409D VAL* 4.3 15.0 - - + -
411D ASP* 3.0 22.9 + - - +
454D LYS* 4.0 28.0 - - + -
455D PHE 3.2 5.6 - - - +
456D GLY* 3.4 31.9 - - - -
619D PHE* 3.7 9.9 - + + -
621D TYR* 1.3 78.4 - - - +
623D ALA* 1.3 59.8 + - - +
624D TYR* 3.3 32.2 - - + +
726D LYS* 3.2 23.9 + - - -
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Residues in contact with ALA 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D VAL* 3.9 1.6 - - - +
454D LYS* 3.5 3.6 - - - -
455D PHE* 2.7 37.7 + - - +
457D ILE* 4.5 7.8 - - + +
621D TYR* 4.3 1.9 + - + -
622D PHE* 1.3 73.3 - - - +
624D TYR* 1.3 60.9 + - - +
650D ASP* 4.2 12.3 - - - +
726D LYS* 4.4 5.6 - - + -
727D ALA 4.1 12.3 - - - +
731D PRO* 3.7 33.4 - - + -
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Residues in contact with TYR 624 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409D VAL* 3.1 20.8 - - - +
411D ASP* 2.7 41.6 + - - -
412D CYS* 3.3 24.8 - - - -
413D VAL* 4.1 20.2 - - + -
414D LEU* 3.6 27.1 - - + -
417D LEU* 4.9 1.8 - - + -
453D VAL* 3.2 11.9 - - - +
454D LYS* 3.5 22.2 - - + +
622D PHE* 3.3 35.2 - - + +
623D ALA* 1.3 73.6 - - - +
625D GLY* 1.3 59.5 + - - +
649D HIS* 3.4 12.8 - - - -
650D ASP* 3.0 37.8 + - + +
726D LYS* 4.2 0.9 - - - -
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Residues in contact with GLY 625 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D LEU* 3.7 4.9 - - - +
417D LEU* 4.1 8.7 - - - +
452D PRO* 3.5 1.7 - - - +
453D VAL* 2.7 36.3 + - - +
624D TYR* 1.3 78.3 - - - +
626D ALA* 1.3 62.4 + - - +
648D LEU 3.5 11.2 - - - -
649D HIS* 3.5 14.1 - - - -
650D ASP 4.3 0.4 - - - -
735D LEU* 4.0 4.9 - - - -
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Residues in contact with ALA 626 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417D LEU* 3.5 20.6 - - + -
418D VAL* 4.0 16.6 - - + -
421D LEU* 3.5 16.7 - - + +
450D LEU* 4.9 3.4 - - + -
451D SER 3.4 11.2 - - - +
452D PRO* 4.5 1.3 - - + -
625D GLY* 1.3 74.2 - - - +
627D ALA* 1.3 60.6 + - - +
647D ILE* 3.4 5.2 - - - +
648D LEU 2.9 31.2 + - - +
735D LEU* 3.5 8.7 - - - +
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Residues in contact with ALA 627 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421D LEU* 4.0 0.7 - - - -
450D LEU* 3.2 3.1 - - - +
451D SER 2.9 32.5 + - - +
626D ALA* 1.3 76.9 - - - +
628D ILE* 1.3 63.5 + - - +
645D THR* 4.6 5.4 - - + -
646D ASP 3.3 4.7 - - - -
647D ILE* 3.6 21.8 - - + -
735D LEU* 3.8 19.7 - - + +
738D SER* 3.3 20.7 - - - +
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Residues in contact with ILE 628 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421D LEU* 3.8 23.8 - - + -
422D GLN* 3.9 18.4 - - + -
425D ALA* 3.8 17.3 - - + -
427D PHE* 3.8 20.0 - - + -
430D ARG* 4.2 7.4 - - - +
448D ILE* 3.6 32.3 - - + -
449D ALA 3.2 9.2 - - - +
450D LEU* 3.7 17.9 - - + -
627D ALA* 1.3 77.6 - - - +
629D THR* 1.3 64.1 + - - +
644D ARG 3.7 1.0 - - - +
645D THR* 3.2 5.8 - - - +
646D ASP* 2.9 39.2 + - + +
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Residues in contact with THR 629 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448D ILE* 3.3 4.6 - - - +
449D ALA 3.0 31.7 + - - -
628D ILE* 1.3 73.4 - - - +
630D GLU* 1.3 61.6 + - - +
631D VAL* 3.8 17.7 - - + -
642D ILE* 3.9 13.7 - - + -
644D ARG 3.3 2.5 - - - -
645D THR* 3.5 2.1 + - - +
668D TYR* 2.5 33.1 + - - +
738D SER* 3.0 31.7 + - - +
739D ALA* 3.6 16.3 + - + -
742D ALA* 3.2 5.6 - - - +
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Residues in contact with GLU 630 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462C PRO 5.1 5.9 - - - -
430D ARG* 2.9 34.2 + - - +
434D ILE* 4.1 15.9 - - + +
446D ARG* 2.7 35.2 + - - -
447D GLY 3.3 8.3 - - - +
448D ILE* 4.2 5.8 - - + +
629D THR* 1.3 72.8 - - - +
631D VAL* 1.3 66.7 + - - +
642D ILE* 3.6 2.8 - - - +
643D LEU* 2.7 46.4 + - + +
644D ARG* 2.7 25.7 + - - +
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Residues in contact with VAL 631 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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446D ARG* 3.3 10.7 - - - +
447D GLY 2.8 29.2 + - - +
629D THR* 3.8 18.8 - - + -
630D GLU* 1.3 82.3 - - - +
632D VAL* 1.3 61.9 + - - +
633D ILE* 4.5 0.2 - - + -
641D ARG 3.3 14.4 - - - +
642D ILE* 4.2 10.5 - - + -
643D LEU* 4.2 2.7 - - - -
739D ALA 4.3 5.8 - - - +
742D ALA* 3.6 29.6 - - + +
743D LEU* 3.5 34.3 - - + -
746D ALA* 4.1 9.6 - - + -
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Residues in contact with VAL 632 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C VAL* 3.9 22.5 - - + +
460C VAL* 3.8 20.2 - - + -
437D TRP* 4.2 10.8 - - + -
444D LEU* 5.1 2.9 - - + -
445D ALA 3.3 11.0 - - - +
446D ARG* 3.2 34.1 - - + +
631D VAL* 1.3 71.1 - - - +
633D ILE* 1.3 64.8 + - - +
640D ASN* 3.2 6.9 - - - +
641D ARG* 3.1 29.8 + - + +
643D LEU* 3.4 29.8 - - + -
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Residues in contact with ILE 633 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457C VAL* 4.0 4.9 - - - -
444D LEU* 3.4 7.5 - - - +
445D ALA* 2.9 45.4 + - + +
631D VAL* 4.5 0.2 - - + -
632D VAL* 1.3 80.0 - - - +
634D ASP* 1.3 62.3 + - - +
635D ARG* 3.5 2.1 + - + +
639D GLU 3.5 6.1 - - - +
640D ASN* 3.8 5.6 - - + -
743D LEU* 3.4 31.4 - - + -
746D ALA* 3.6 35.2 - - + +
747D CYS* 4.1 2.2 - - - +
750D CYS* 4.7 1.8 - - - -
766D VAL* 4.0 17.0 - - + -
770D VAL* 3.5 31.9 - - + -
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Residues in contact with ASP 634 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445C ARG* 2.3 36.1 + - - +
455C VAL 3.8 7.7 - - - +
457C VAL* 3.4 18.0 - - + +
443D THR* 3.5 19.8 - - - +
444D LEU* 4.2 1.8 - - - -
633D ILE* 1.3 74.1 - - - +
635D ARG* 1.3 62.1 + - - +
636D LEU* 3.2 11.6 + - - +
637D THR* 2.5 21.2 + - - +
638D GLY* 3.0 26.2 + - - -
639D GLU* 2.8 19.6 + - + +
767D LEU* 5.1 0.3 - - - +
770D VAL* 5.3 1.4 - - - +
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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