Contacts of the strand formed by residues 621 - 634 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407F GLN* 5.3 1.3 - - - +
411F ASP* 3.8 10.8 - - + +
456F GLY* 3.6 3.6 - - - -
457F ILE* 3.0 48.5 + - + -
534F ASP* 2.7 28.0 + - - -
619F PHE* 3.3 4.6 - - - +
620F LEU* 1.3 98.3 - - + +
622F PHE* 1.3 80.6 + - - +
623F ALA* 4.8 0.9 - - + -
717F ASN* 3.3 31.6 - - - +
719F GLU* 4.2 8.3 - - + -
721F THR* 3.7 11.4 - - + -
725F SER 4.3 0.2 + - - -
726F LYS* 3.4 22.8 - - + -
727F ALA* 2.7 29.0 + - - +
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Residues in contact with PHE 622 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314F HIS* 5.7 0.9 - - - -
403F THR* 4.2 3.4 - - + -
405F TYR* 3.3 26.5 - - - -
407F GLN* 3.7 37.5 - - + -
408F GLU 4.6 4.7 - - - -
409F VAL* 4.1 14.8 - - + -
411F ASP* 3.0 24.3 + - - +
454F LYS* 3.4 29.6 - - + -
455F PHE 3.2 6.5 - - - +
456F GLY* 3.6 27.4 - - - -
619F PHE* 4.1 4.3 - + - -
621F TYR* 1.3 82.6 - - - +
623F ALA* 1.3 52.6 + - - +
624F TYR* 3.5 25.8 - - + +
726F LYS* 2.8 32.2 + - - -
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Residues in contact with ALA 623 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453F VAL* 3.8 1.7 - - - +
454F LYS* 3.5 4.2 - - - -
455F PHE* 2.8 34.3 + - - +
457F ILE* 4.6 5.8 - - + +
621F TYR* 4.5 1.1 - - + -
622F PHE* 1.3 74.9 - - - +
624F TYR* 1.3 61.1 + - - +
649F HIS* 4.9 1.1 - - - +
650F ASP* 4.2 12.8 - - - +
726F LYS* 4.2 11.4 - - + +
727F ALA 4.1 11.7 - - - +
731F PRO* 3.9 30.1 - - + -
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Residues in contact with TYR 624 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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409F VAL* 3.1 20.8 - - - +
411F ASP* 2.9 41.8 + - - -
412F CYS* 3.4 24.3 - - - -
413F VAL* 4.4 15.3 - - + -
414F LEU* 3.7 22.2 - - + +
417F LEU* 4.6 2.7 - - + -
453F VAL* 3.2 18.2 - - - +
454F LYS* 3.6 19.4 - - + +
622F PHE* 3.5 32.0 - - + +
623F ALA* 1.3 75.3 - - - +
625F GLY* 1.3 59.1 + - - +
649F HIS* 3.4 12.7 + - - -
650F ASP* 3.0 43.3 + - + +
726F LYS* 4.3 0.2 - - - -
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Residues in contact with GLY 625 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414F LEU* 4.0 4.4 - - - +
417F LEU* 3.9 10.6 - - - +
452F PRO* 3.5 1.4 - - - +
453F VAL* 2.8 31.2 + - - +
624F TYR* 1.3 78.6 - - - +
626F ALA* 1.3 60.8 + - - +
648F LEU 3.4 13.2 - - - -
649F HIS* 3.7 13.7 - - - -
735F LEU* 4.1 4.7 - - - -
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Residues in contact with ALA 626 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417F LEU* 3.7 12.3 - - + +
418F VAL* 4.2 15.9 - - + -
421F LEU* 3.7 19.1 - - + +
450F LEU* 4.3 5.2 - - + -
451F SER 3.2 14.1 - - - +
452F PRO* 4.3 2.7 - - + -
625F GLY* 1.3 76.8 - - - +
627F ALA* 1.3 64.2 - - - +
647F ILE* 3.5 5.9 - - - +
648F LEU 3.1 29.2 + - - +
735F LEU* 3.9 6.9 - - - +
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Residues in contact with ALA 627 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421F LEU* 4.1 1.3 - - - -
450F LEU* 3.3 0.6 - - - -
451F SER 3.0 30.9 + - - +
626F ALA* 1.3 77.0 - - - +
628F ILE* 1.3 62.5 - - - +
645F THR* 4.5 6.1 - - + -
646F ASP 3.3 5.6 - - - +
647F ILE* 3.7 21.3 - - + -
668F TYR* 4.6 0.7 - - + -
735F LEU* 3.7 19.3 - - + +
738F SER* 3.1 26.1 - - - +
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Residues in contact with ILE 628 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421F LEU* 3.8 20.3 - - + +
422F GLN* 3.8 17.5 - - + -
425F ALA* 4.0 15.0 - - + -
427F PHE* 4.0 14.1 - - + -
430F ARG* 3.7 24.0 - - - +
448F ILE* 3.7 23.3 - - + -
449F ALA 3.0 4.7 - - - +
450F LEU* 3.4 40.4 - - + -
627F ALA* 1.3 71.7 - - - +
629F THR* 1.3 64.3 + - - +
644F ARG 3.7 0.9 - - - +
645F THR* 3.3 3.6 - - - +
646F ASP* 2.8 38.2 + - + +
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Residues in contact with THR 629 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448F ILE* 3.3 6.2 - - - +
449F ALA 2.9 30.6 + - - -
627F ALA 3.8 0.2 + - - -
628F ILE* 1.3 76.2 + - - +
630F GLU* 1.3 63.8 + - - +
631F VAL* 4.1 7.4 - - + -
642F ILE* 3.6 20.0 - - + -
644F ARG 3.3 2.2 - - - -
645F THR* 3.8 3.1 + - - +
668F TYR* 2.9 32.1 + - - +
738F SER* 2.7 36.9 + - - -
739F ALA* 3.7 14.7 + - + -
742F ALA* 3.3 3.5 - - - +
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Residues in contact with GLU 630 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462E PRO 5.1 4.2 - - - -
430F ARG* 3.5 25.0 + - - +
434F ILE* 3.9 12.7 - - + +
446F ARG* 2.5 50.7 + - - +
447F GLY 3.3 13.3 - - - +
448F ILE* 3.8 18.8 - - + -
629F THR* 1.3 74.3 - - - +
631F VAL* 1.3 55.4 + - - +
642F ILE* 3.4 4.3 - - - +
643F LEU* 2.7 41.5 + - - +
644F ARG* 2.8 26.2 + - - +
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Residues in contact with VAL 631 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445F ALA 4.0 0.2 - - - +
446F ARG* 3.1 7.3 - - - +
447F GLY 2.8 38.6 + - - +
629F THR* 4.1 10.1 - - + -
630F GLU* 1.3 79.8 - - - +
632F VAL* 1.3 59.9 + - - +
641F ARG 3.2 8.5 - - - +
642F ILE* 3.7 26.0 - - + -
643F LEU* 4.0 5.4 - - - +
739F ALA 4.2 12.3 - - - +
742F ALA* 3.6 12.1 - - + +
743F LEU* 3.5 47.3 - - + +
746F ALA* 4.2 4.5 - - + -
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Residues in contact with VAL 632 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457E VAL* 3.7 24.2 - - + +
460E VAL* 4.0 26.9 - - + -
437F TRP* 4.2 8.3 - - + -
444F LEU* 4.8 3.4 - - + -
445F ALA 3.3 7.0 - - - +
446F ARG* 3.7 24.9 - - + -
631F VAL* 1.3 74.6 - - - +
633F ILE* 1.3 64.8 + - - +
640F ASN* 3.2 7.3 - - - +
641F ARG* 2.9 31.6 + - + +
643F LEU* 3.6 29.2 - - + -
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Residues in contact with ILE 633 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457E VAL* 4.0 4.8 - - - +
444F LEU* 3.5 11.3 - - - +
445F ALA* 2.8 44.0 + - + +
632F VAL* 1.3 75.5 - - - +
634F ASP* 1.3 62.3 + - - +
635F ARG* 5.1 1.1 - - + +
639F GLU 3.5 6.1 - - - +
640F ASN* 3.5 9.2 - - + +
743F LEU* 3.5 33.2 - - + +
746F ALA* 3.8 32.1 - - + +
747F CYS* 4.2 2.9 - - - -
750F CYS* 4.9 2.2 - - - -
766F VAL* 3.8 18.4 - - + -
770F VAL* 3.5 32.3 - - + -
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Residues in contact with ASP 634 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445E ARG* 2.3 35.2 + - - -
455E VAL 3.4 9.7 - - - +
457E VAL* 3.7 13.9 - - + -
443F THR* 3.3 28.0 - - - +
444F LEU* 3.6 1.3 - - - +
633F ILE* 1.3 77.3 - - - +
635F ARG* 1.3 58.5 + - - +
636F LEU* 3.0 6.9 + - - +
637F THR* 2.7 24.7 + - - +
638F GLY* 3.0 22.9 + - - +
639F GLU* 3.1 15.2 + - + +
767F LEU* 4.9 1.0 - - - +
770F VAL* 5.0 2.6 - - - +
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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