Contacts of the strand formed by residues 629 - 645 (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 LEU 629 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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623A GLU* 3.6 2.9 - - - +
624A TYR* 2.7 69.4 + - + +
625A LEU* 4.6 5.6 - - + -
627A GLY 3.2 0.8 - - - -
628A ARG* 1.3 79.1 - - - +
630A ASN* 1.3 63.8 + - - +
631A THR* 5.2 0.2 - - + -
677A ILE* 3.7 31.2 - - + -
678A SER 3.5 22.4 - - - +
679A GLY 4.0 5.4 - - - +
680A GLU 3.5 27.1 - - - +
681A LEU* 4.4 10.5 - - + -
687A VAL* 4.9 0.9 - - + -
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Residues in contact with ASN 630 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A THR* 3.3 23.1 + - - +
149A PRO* 4.6 3.2 - - + +
162A PRO* 4.0 33.8 - - + +
163A ARG* 4.3 5.1 - - - +
622A GLY 3.4 5.7 + - - +
623A GLU* 4.0 27.0 + - - +
627A GLY* 3.6 18.0 + - - +
629A LEU* 1.3 73.6 - - - +
631A THR* 1.3 66.3 + - - +
677A ILE* 3.3 5.0 - - - +
678A SER* 3.0 33.5 + - - +
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Residues in contact with THR 631 (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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583A TYR* 4.4 3.3 - - - -
621A LYS* 3.1 4.7 - - - +
622A GLY* 2.6 45.9 + - - +
624A TYR* 2.8 39.6 + - + +
629A LEU* 5.0 1.8 - - + -
630A ASN* 1.3 78.8 - - - +
632A SER* 1.3 61.9 + - - +
676A GLU 3.5 5.8 - - - -
677A ILE* 3.5 29.6 - - + -
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Residues in contact with SER 632 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A TYR* 5.7 2.5 - - - -
620A ILE 3.3 5.6 - - - -
621A LYS* 3.7 25.4 - - - -
631A THR* 1.3 78.1 - - - +
633A LEU* 1.3 62.1 + - - +
634A ALA* 4.3 1.3 - - - -
674A GLU 4.4 0.6 + - - -
675A ALA* 3.2 4.9 - - - +
676A GLU* 2.9 54.6 + - - +
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Residues in contact with LEU 633 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586A TYR* 4.9 0.8 + - - -
619A GLY* 3.5 1.9 - - - -
620A ILE* 2.9 49.1 + - + +
632A SER* 1.3 75.3 - - - +
634A ALA* 1.3 69.7 - - - +
673A TYR* 4.8 14.8 - - + -
674A GLU 3.3 13.9 - - - +
675A ALA* 4.4 11.2 - - + -
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Residues in contact with ALA 634 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A SER* 4.1 7.4 - - - +
586A TYR* 3.4 24.9 - - - +
617A GLU* 3.6 15.0 - - - +
618A ILE 3.7 6.3 - - - +
632A SER* 5.4 2.0 - - - -
633A LEU* 1.3 79.4 - - - +
635A TYR* 1.3 61.7 + - - +
636A PHE* 4.2 2.7 - - + -
673A TYR* 3.1 8.0 - - - +
674A GLU* 2.7 42.6 + - + +
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Residues in contact with TYR 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A TYR 5.6 0.4 - - - -
617A GLU* 3.4 4.0 - - - +
618A ILE* 2.9 50.9 + - + +
634A ALA* 1.3 75.3 - - - +
636A PHE* 1.3 70.9 + - - +
637A GLU* 3.0 29.2 + - + -
671A LYS* 3.9 17.0 - - + +
672A GLY* 3.2 32.3 - - - -
673A TYR* 4.1 12.8 - + + -
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Residues in contact with PHE 636 (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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210A ARG* 3.5 64.2 - - + +
615A ASN* 4.1 5.8 - - - +
616A TYR 3.2 10.3 - - - +
617A GLU* 4.2 6.1 - - + +
634A ALA* 4.7 2.7 - - + -
635A TYR* 1.3 84.7 - - - +
637A GLU* 1.3 65.9 + - - +
638A ILE* 4.9 0.9 - - + -
670A THR* 3.6 29.2 - - + -
671A LYS* 3.9 1.2 - - - -
672A GLY* 2.8 58.0 + - - +
673A TYR* 3.6 17.0 - - - -
674A GLU* 4.1 6.7 - - + -
692A THR* 4.4 7.9 - - + -
693A HIS 4.0 6.1 - - - -
694A LYS* 5.0 2.9 - - + -
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Residues in contact with GLU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614A GLN 3.6 1.0 - - - +
615A ASN* 3.5 3.3 - - - -
616A TYR* 2.8 45.6 + - + +
635A TYR* 3.0 30.8 + - + -
636A PHE* 1.3 76.0 - - - +
638A ILE* 1.3 61.6 + - - +
639A HIS* 3.3 32.8 + - + +
669A LYS* 4.5 5.6 - - + +
670A THR 3.1 13.5 - - - +
671A LYS* 3.8 17.4 + - + +
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Residues in contact with ILE 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A ARG* 3.8 37.5 - - + +
212A PHE* 3.6 28.0 - - + -
251A GLY 4.1 14.8 - - - +
262A LEU* 3.9 22.9 - - + -
263A GLY 4.7 2.0 - - - +
614A GLN 3.4 4.3 - - - +
615A ASN* 3.6 32.5 - - + +
636A PHE* 5.1 1.1 - - + -
637A GLU* 1.3 72.9 - - - +
639A HIS* 1.3 68.9 + - - +
640A GLU 4.5 0.2 - - - +
668A ALA 3.7 0.5 - - - +
669A LYS* 3.2 7.3 - - - -
670A THR* 2.7 47.0 + - + +
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Residues in contact with HIS 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613A GLY* 3.0 3.7 - - - -
614A GLN* 2.8 54.4 + - - +
616A TYR* 4.0 26.4 + + + -
637A GLU* 3.3 35.1 + - + +
638A ILE* 1.3 81.3 - - - +
640A GLU* 1.3 60.1 + - - +
641A GLU* 4.0 4.9 - - - +
668A ALA 3.8 4.0 - - - +
669A LYS* 3.4 35.5 + - + -
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Residues in contact with GLU 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A PHE* 3.1 30.4 - - + -
262A LEU* 4.1 10.1 - - + +
611A ASP* 2.4 33.4 - - - +
612A GLU 3.3 13.7 - - - +
613A GLY* 4.1 1.1 - - - -
638A ILE 3.9 1.0 + - - -
639A HIS* 1.3 72.8 - - - +
641A GLU* 1.3 67.3 + - - +
643A ARG* 3.0 42.8 + - + +
667A LYS* 3.2 8.7 - - - +
668A ALA* 2.8 40.8 + - + +
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Residues in contact with GLU 641 (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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611A ASP* 3.7 1.9 - - - +
612A GLU* 2.9 59.2 + - + +
614A GLN* 2.6 45.3 + - - +
639A HIS* 3.7 8.4 - - - +
640A GLU* 1.3 78.0 - - - +
642A ASN* 1.3 72.4 + - - +
643A ARG 3.4 2.4 + - - -
666A ILE 3.6 2.5 - - - -
667A LYS* 3.9 26.5 - - + -
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Residues in contact with ASN 642 (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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596A GLN* 3.4 13.0 - - - +
608A LEU* 5.0 1.6 - - + +
609A GLU* 3.4 42.5 - - + +
610A PRO 3.1 18.9 + - - +
611A ASP* 3.7 5.4 - - - -
612A GLU* 3.2 16.0 + - - -
641A GLU* 1.3 78.0 - - - +
643A ARG* 1.3 63.7 + - - +
644A ALA* 3.2 3.5 + - - -
665A GLY* 3.9 20.0 - - - +
666A ILE 2.7 12.0 + - - -
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Residues in contact with ARG 643 (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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211A GLY 4.5 4.9 + - - -
212A PHE* 3.9 18.2 - - - -
611A ASP* 4.0 4.5 - - - +
640A GLU* 3.0 46.7 + - + +
641A GLU 3.4 1.4 - - - -
642A ASN* 1.3 71.8 - - - +
644A ALA* 1.3 73.5 + - - +
645A GLU* 3.1 1.9 + - - -
666A ILE* 2.8 51.6 + - + +
667A LYS 5.0 0.2 - - - +
668A ALA* 4.0 14.2 - - + +
696A ILE* 4.2 4.2 - - - +
698A ASP* 5.2 2.7 - - - -
704A VAL* 3.7 40.4 - - - +
705A SER* 4.6 1.6 + - - -
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Residues in contact with ALA 644 (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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596A GLN* 3.8 13.9 + - - +
600A TYR* 3.8 39.9 - - + -
608A LEU* 3.9 11.9 - - + -
611A ASP* 4.6 2.4 + - - +
642A ASN 3.2 5.9 + - - -
643A ARG* 1.3 79.0 + - - +
645A GLU* 1.3 60.5 + - - +
646A GLU 4.2 0.2 - - - -
663A TYR* 4.3 4.0 - - + -
664A LYS 3.6 4.9 - - - -
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Residues in contact with GLU 645 (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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643A ARG* 3.1 0.9 + - + -
644A ALA* 1.3 69.4 - - - +
646A GLU* 1.3 76.9 + - + +
647A ASP 2.9 6.4 + - - -
663A TYR* 3.6 3.4 - - - -
664A LYS* 2.4 71.1 + - + +
666A ILE* 3.8 35.1 - - + +
698A ASP* 4.1 4.2 - - - +
702A LYS* 3.8 26.2 + - - +
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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
------------------------------------------------------------
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