Contacts of the strand formed by residues 664 - 682 (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 LYS 664 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602A ASP* 5.6 0.2 - - - -
608A LEU* 3.6 5.6 - - - -
643A ARG 3.5 0.2 - - - +
644A ALA* 3.4 1.0 - - - -
645A GLU* 2.4 66.9 + - + +
647A ASP* 4.1 29.6 - - + +
648A ALA 5.8 0.2 - - - +
663A TYR* 1.3 74.8 - - - +
665A GLY* 1.3 60.7 + - - +
666A ILE* 3.6 15.2 + - + +
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Residues in contact with GLY 665 (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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608A LEU* 3.5 26.0 - - - +
642A ASN* 3.9 21.0 - - - +
643A ARG 3.8 2.9 - - - -
664A LYS* 1.3 73.5 - - - +
666A ILE* 1.3 64.7 + - - +
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Residues in contact with ILE 666 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A GLU* 3.4 0.9 - - - -
642A ASN 2.7 30.7 + - - -
643A ARG* 2.8 43.8 + - + +
645A GLU* 3.8 35.9 - - + +
664A LYS* 4.4 24.7 - - + +
665A GLY* 1.3 77.6 - - - +
667A LYS* 1.3 65.5 + - - +
698A ASP* 3.6 37.0 - - + +
699A ASP* 4.1 13.7 - - - +
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Residues in contact with LYS 667 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A GLU* 3.2 9.9 - - - +
641A GLU* 3.9 27.8 - - + -
643A ARG* 5.3 0.9 - - - -
666A ILE* 1.3 86.1 - - - +
668A ALA* 1.3 61.4 + - - +
698A ASP* 3.3 9.7 - - - +
699A ASP* 3.1 45.9 + - + +
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Residues in contact with ALA 668 (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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212A PHE* 6.1 0.2 - - - -
638A ILE 3.7 0.9 - - - +
639A HIS* 3.8 1.7 - - - -
640A GLU* 2.8 54.7 + - + +
643A ARG* 4.0 16.2 - - - +
667A LYS* 1.3 76.8 - - - +
669A LYS* 1.3 65.2 + - - +
696A ILE* 4.6 10.5 - - + -
697A ARG 3.1 15.3 - - - +
698A ASP* 3.9 5.4 - - + +
699A ASP 4.5 1.3 - - - +
704A VAL* 5.5 0.7 - - + -
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Residues in contact with LYS 669 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637A GLU* 4.5 7.2 + - + +
638A ILE 3.2 8.3 - - - +
639A HIS* 3.4 43.3 + - + +
668A ALA* 1.3 76.0 - - - +
670A THR* 1.3 69.5 + - - +
671A LYS* 4.0 23.3 + - - +
695A ILE 3.7 1.2 - - - +
696A ILE* 3.1 8.1 - - - -
697A ARG* 2.7 39.6 + - + +
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Residues in contact with THR 670 (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* 2.9 33.0 + - + +
212A PHE* 3.9 1.2 - - - -
636A PHE* 3.6 29.4 - - + -
637A GLU* 3.1 12.1 - - - +
638A ILE* 2.7 45.8 + - + +
669A LYS* 1.3 73.6 - - - +
671A LYS* 1.3 66.6 + - - +
694A LYS* 4.8 4.9 - - + -
695A ILE 3.5 5.2 - - - +
696A ILE* 3.1 26.1 - - + +
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Residues in contact with LYS 671 (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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635A TYR* 3.9 13.7 - - + +
636A PHE 3.9 3.6 - - - -
637A GLU* 3.8 24.0 + - + +
669A LYS* 4.0 23.7 + - + +
670A THR* 1.3 80.7 - - - +
672A GLY* 1.3 57.8 + - - +
693A HIS* 4.8 2.8 + - - -
694A LYS* 3.5 1.7 - - - -
695A ILE* 2.9 36.0 + - + +
697A ARG* 6.5 0.9 - - - +
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Residues in contact with GLY 672 (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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635A TYR* 3.2 14.3 - - - -
636A PHE* 2.8 47.5 + - - +
671A LYS* 1.3 75.1 - - - +
673A TYR* 1.3 61.7 - - - -
693A HIS* 3.0 22.4 - - - -
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Residues in contact with TYR 673 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633A LEU* 4.8 13.9 - - + -
634A ALA 3.1 17.3 - - - +
635A TYR* 4.1 15.5 - + + -
636A PHE* 3.7 4.3 - - - -
672A GLY* 1.3 75.7 - - - +
674A GLU* 1.3 64.0 + - - +
675A ALA* 6.2 0.9 - - + -
691A TYR* 4.0 24.6 + + - -
692A THR* 3.5 1.0 - - - +
693A HIS* 2.8 71.6 + + + +
711A ASP* 4.9 0.7 + - - -
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Residues in contact with GLU 674 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A SER* 3.9 6.2 + - - -
194A GLY* 3.5 8.1 - - - -
210A ARG* 3.0 26.1 + - - +
250A LYS* 2.7 28.7 + - - +
632A SER* 3.9 1.4 + - - +
633A LEU* 3.3 5.1 - - - +
634A ALA* 2.7 44.7 + - + +
636A PHE* 4.1 7.6 - - + -
673A TYR* 1.3 77.4 - - - +
675A ALA* 1.3 61.3 + - - +
676A GLU* 3.1 24.9 - - + +
691A TYR 3.2 5.6 - - - +
692A THR* 2.7 34.8 + - + +
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Residues in contact with ALA 675 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A SER 3.2 9.0 - - - +
633A LEU* 4.4 14.8 - - + -
673A TYR* 5.5 1.3 - - + -
674A GLU* 1.3 74.4 - - - +
676A GLU* 1.3 63.3 + - - +
690A GLY* 2.9 2.9 - - - -
691A TYR* 2.5 53.4 + - + +
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Residues in contact with GLU 676 (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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168A SER* 6.3 1.6 - - - -
169A ILE 4.7 2.9 - - - +
170A THR* 2.4 34.9 + - - +
193A PRO* 4.1 12.8 - - + +
250A LYS* 2.9 25.1 + - - -
630A ASN 5.5 0.2 - - - -
631A THR* 3.5 2.9 - - - -
632A SER* 2.9 47.1 + - - +
674A GLU* 3.1 19.7 - - + +
675A ALA* 1.3 78.8 - - - +
677A ILE* 1.3 63.7 + - - +
688A GLN* 5.3 1.5 + - + -
689A ALA 3.2 14.8 - - - +
690A GLY* 3.8 2.8 - - - -
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Residues in contact with ILE 677 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A LEU* 3.7 22.9 - - + -
630A ASN 3.3 7.4 - - - +
631A THR* 3.5 26.5 - - + -
676A GLU* 1.3 77.2 - - - +
678A SER* 1.3 66.9 + - - +
681A LEU* 4.0 17.9 - - + -
687A VAL* 4.7 8.1 - - + -
688A GLN* 3.3 1.6 - - - +
689A ALA* 2.8 52.0 + - + +
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Residues in contact with SER 678 (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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147A TYR 3.6 16.8 - - - -
148A THR* 2.7 30.3 + - - -
149A PRO* 4.7 3.1 - - - +
629A LEU* 3.5 5.8 - - - +
630A ASN* 3.0 34.6 + - - +
677A ILE* 1.3 79.4 - - - +
679A GLY* 1.3 60.0 + - - +
687A VAL* 3.1 10.5 - - - -
688A GLN* 3.9 18.1 + - - -
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Residues in contact with GLY 679 (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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148A THR* 3.7 12.0 - - - +
628A ARG 3.3 10.3 - - - -
629A LEU* 4.0 2.2 - - - -
678A SER* 1.3 75.3 - - - +
680A GLU* 1.3 61.5 + - - -
681A LEU 3.6 0.5 + - - -
686A GLN* 3.3 21.3 + - - -
687A VAL* 2.8 37.6 + - - +
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Residues in contact with GLU 680 (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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625A LEU* 3.8 18.2 - - + +
628A ARG* 3.0 52.1 + - + +
629A LEU* 3.5 26.4 - - - +
679A GLY* 1.3 69.8 - - - -
681A LEU* 1.3 58.6 + - - +
682A ALA* 3.0 24.5 - - - +
683A PRO* 3.2 34.1 - - + +
685A TRP 3.4 3.4 - - - +
686A GLN* 3.2 16.2 - - - +
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Residues in contact with LEU 681 (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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625A LEU* 5.4 3.5 - - - +
629A LEU* 4.4 10.0 - - + +
677A ILE* 4.0 21.1 - - + -
679A GLY 3.6 0.6 + - - -
680A GLU* 1.3 73.9 - - - +
682A ALA* 1.3 63.1 + - - +
685A TRP* 3.0 48.8 + - + +
687A VAL* 3.5 44.4 - - + -
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Residues in contact with ALA 682 (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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625A LEU* 6.1 0.7 - - - -
680A GLU* 3.0 15.6 - - - +
681A LEU* 1.3 79.0 - - - +
683A PRO* 1.4 80.7 - - + +
684A GLY 3.5 2.0 - - - +
685A TRP* 2.8 34.8 + - + +
719A TYR* 6.1 1.3 - - + -
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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