Contacts of the strand formed by residues 640 - 650 (chain H) 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 ASN 640 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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357G PHE* 3.3 21.4 - - - -
457G VAL* 3.8 5.3 - - - +
632H VAL 2.8 16.4 - - - +
633H ILE* 3.5 14.8 - - + -
638H GLY 2.8 21.6 + - - -
639H GLU* 1.3 76.5 - - - +
641H ARG* 1.3 61.2 + - - +
676H THR* 5.3 6.4 - - - +
677H THR* 6.0 1.0 - - - +
743H LEU* 4.1 22.8 - - + +
761H ALA 4.7 2.8 + - - +
763H PRO* 3.7 23.4 - - - +
766H VAL* 4.1 7.5 - - - +
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Residues in contact with ARG 641 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357G PHE* 4.8 6.3 - - + -
457G VAL* 4.0 12.1 + - + +
458G LEU* 3.7 43.7 + - + +
460G VAL 4.8 4.8 + - - -
462G PRO* 6.2 0.4 - - - -
631H VAL* 3.0 30.5 - - - +
632H VAL* 2.8 26.8 + - + +
640H ASN* 1.3 77.0 - - - +
642H ILE* 1.3 68.5 + - - +
643H LEU* 3.3 26.3 + - - +
702H SER* 3.6 15.1 + - - +
703H ASP* 6.0 2.7 - - - +
704H ARG 5.4 0.4 + - - -
706H ARG* 2.7 59.2 - - - +
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Residues in contact with ILE 642 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629H THR* 3.7 13.9 - - + -
630H GLU 3.6 3.1 - - - +
631H VAL* 3.7 13.7 - - + -
641H ARG* 1.3 81.5 - - - +
643H LEU* 1.3 60.5 + - - +
644H ARG 4.4 1.6 - - - +
645H THR* 3.6 24.9 - - - +
668H TYR* 4.5 5.4 - - + +
672H ALA* 4.1 16.4 - - + -
676H THR* 5.0 11.7 - - + +
703H ASP 4.4 16.3 + - - +
704H ARG 4.1 2.3 - - - +
705H PRO* 3.4 14.1 - - + +
706H ARG 3.3 14.4 + - - -
739H ALA* 4.0 22.0 - - + -
743H LEU* 6.1 0.9 - - + -
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Residues in contact with LEU 643 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460G VAL* 3.8 26.5 - - + +
461G MET 4.2 4.7 - - - +
462G PRO* 3.8 27.9 - - + +
446H ARG* 3.5 29.4 - - - +
630H GLU* 2.8 22.4 + - + +
631H VAL 4.0 7.9 - - - -
632H VAL* 3.5 32.8 - - + -
641H ARG* 3.3 20.6 + - - +
642H ILE* 1.3 73.7 - - - +
644H ARG* 1.3 59.5 + - - +
706H ARG* 3.0 13.9 - - + +
707H ILE 3.0 19.8 + - - -
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Residues in contact with ARG 644 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
462G PRO 5.1 4.5 - - - -
424H SER 4.9 2.8 + - - -
425H ALA* 3.9 14.8 + - - +
426H ASN* 5.7 1.0 - - - +
430H ARG* 3.2 45.2 + - - +
628H ILE 3.8 0.9 - - - +
629H THR* 3.5 1.4 - - - +
630H GLU* 2.8 40.5 + - - +
642H ILE* 3.5 1.4 - - - -
643H LEU* 1.3 82.7 - - + +
645H THR* 1.3 68.8 + - - +
646H ASP* 2.8 36.0 + - - +
705H PRO* 4.2 1.3 - - - -
707H ILE* 3.1 35.9 - - + +
709H ASN* 3.3 17.2 - - - +
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Residues in contact with THR 645 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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627H ALA* 4.7 1.3 - - + -
628H ILE 3.3 9.2 - - - +
629H THR* 4.0 1.7 - - - +
642H ILE* 3.6 3.6 - - - +
644H ARG* 1.3 77.6 + - - +
646H ASP* 1.3 69.7 + - - +
647H ILE* 4.0 20.9 - - + -
668H TYR* 3.1 42.2 + - + +
705H PRO* 3.0 30.6 - - - +
707H ILE 2.6 11.4 + - - +
708H PHE* 4.2 4.5 - - - -
709H ASN* 2.9 25.5 + - - +
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Residues in contact with ASP 646 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421H LEU* 3.6 12.9 - - + +
424H SER* 4.7 3.6 + - - +
425H ALA* 3.6 27.5 - - + +
430H ARG* 3.1 13.0 + - - -
627H ALA* 3.3 5.0 - - - -
628H ILE* 2.9 36.5 + - + +
644H ARG* 2.8 34.0 + - - +
645H THR* 1.3 77.6 - - - +
647H ILE* 1.3 62.5 + - - +
709H ASN* 2.8 30.1 + - - +
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Residues in contact with ILE 647 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421H LEU* 3.8 5.3 - - - +
626H ALA 3.7 4.3 - - - +
627H ALA* 4.1 10.8 - - + -
645H THR* 4.0 10.1 - - + -
646H ASP* 1.3 78.8 - - - +
648H LEU* 1.3 73.0 + - - +
649H HIS* 4.1 2.7 - - + +
664H ILE* 3.6 23.6 - - + -
668H TYR* 3.9 26.5 - - + -
708H PHE* 3.7 29.6 - - + -
709H ASN 2.6 15.4 + - - +
710H VAL* 4.1 10.1 - - + -
711H ALA* 3.0 25.7 + - - +
735H LEU* 3.6 22.0 - - + -
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Residues in contact with LEU 648 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417H LEU* 3.3 50.3 - - + +
420H ARG* 4.1 15.3 - - + -
421H LEU* 3.8 27.0 - - + +
625H GLY* 3.5 0.3 - - - -
626H ALA 3.2 28.3 + - - -
647H ILE* 1.3 75.1 - - - +
649H HIS* 1.3 59.4 + - - +
711H ALA* 3.1 26.9 - - + +
712H LEU 3.9 19.7 - - - +
713H TRP* 3.9 17.7 - - + +
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Residues in contact with HIS 649 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
453H VAL* 5.1 3.1 - - + -
623H ALA* 4.8 1.6 - - - +
624H TYR 3.0 25.2 + - - -
625H GLY* 3.6 9.3 - - - -
647H ILE* 4.1 9.4 - - + +
648H LEU* 1.3 75.4 - - - +
650H ASP* 1.3 78.1 + - - +
651H ALA 3.6 2.3 + - - -
664H ILE* 3.7 27.6 - - + -
711H ALA 3.0 7.5 + - - +
712H LEU* 3.3 9.4 - - - +
713H TRP* 2.7 28.2 + - - -
728H VAL* 3.9 23.6 - - + +
731H PRO* 3.6 34.2 - - + +
732H PRO* 3.7 15.8 - - + +
735H LEU* 4.2 9.3 - - + +
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Residues in contact with ASP 650 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413H VAL* 4.9 3.5 - - + +
417H LEU* 4.3 4.9 - - + +
623H ALA* 4.4 2.8 - - - +
624H TYR* 3.0 38.8 + - + +
648H LEU 4.4 0.2 + - - -
649H HIS* 1.3 84.4 + - - +
651H ALA* 1.3 58.1 - - - +
652H GLY* 3.1 19.4 + - - -
713H TRP* 3.4 36.3 - - + +
715H GLN 4.1 3.1 - - - +
726H LYS* 2.6 44.8 + - - +
727H ALA 5.0 0.7 - - - +
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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