Contacts of the strand formed by residues 583 - 594 (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 TYR 583 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A ARG* 3.3 8.0 + - - -
579A LEU* 2.8 41.4 + - + -
580A ASN* 3.4 20.6 + - - +
582A THR* 1.3 93.2 - - + +
584A SER* 1.3 56.5 + - - +
620A ILE* 3.7 33.4 - - + -
621A LYS 3.5 1.3 - - - -
622A GLY* 3.7 15.9 - - - -
624A TYR* 2.8 34.4 + + - -
631A THR* 4.4 2.9 - - - -
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Residues in contact with SER 584 (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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163A ARG* 2.8 37.8 + - - +
576A VAL* 4.0 13.9 - - - -
577A TYR 3.1 15.3 - - - -
578A ASP* 2.8 20.5 + - - -
579A LEU* 4.2 2.0 - - - +
583A TYR* 1.3 71.9 + - - +
585A VAL* 1.3 63.4 + - - +
586A TYR* 4.9 0.6 - - - -
620A ILE* 3.3 5.5 - - - +
621A LYS* 2.9 35.8 + - - +
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Residues in contact with VAL 585 (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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576A VAL* 3.4 3.3 - - - +
577A TYR* 2.6 63.4 + - + +
579A LEU* 4.4 17.8 - - + +
584A SER* 1.3 79.1 - - - +
586A TYR* 1.3 62.2 + - - +
618A ILE* 6.0 7.6 - - + -
619A GLY 3.1 14.4 - - - +
620A ILE* 4.1 16.8 - - + -
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Residues in contact with TYR 586 (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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163A ARG 5.9 0.9 - - - +
165A THR 5.0 0.2 - - - -
166A PRO* 3.7 31.4 - - + -
167A GLN 4.0 2.1 - - - -
168A SER* 4.1 2.3 + - - -
575A ALA 3.1 16.2 - - - +
576A VAL* 3.7 16.8 - - + -
577A TYR 4.8 0.2 - - - +
584A SER* 4.9 0.9 - - - -
585A VAL* 1.3 78.2 - - - +
587A ALA* 1.3 65.6 + - - +
617A GLU* 2.8 40.0 + - + -
618A ILE* 3.4 6.8 - - - +
619A GLY* 2.8 65.4 + - - -
620A ILE* 3.8 2.7 - - - -
621A LYS* 3.8 42.7 - - + -
632A SER* 5.7 1.6 - - - -
633A LEU 4.9 1.1 - - - -
634A ALA* 3.4 14.9 - - - +
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Residues in contact with ALA 587 (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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166A PRO* 4.2 1.4 - - - +
574A GLY* 3.2 1.7 - - - -
575A ALA* 2.8 37.2 + - + +
586A TYR* 1.3 79.7 - - - +
588A SER* 1.3 62.3 + - - +
617A GLU 3.2 12.1 - - - +
618A ILE* 4.2 12.3 - - + -
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Residues in contact with SER 588 (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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166A PRO* 2.9 29.4 + - - -
167A GLN* 4.2 3.7 - - - +
572A TYR* 5.4 1.6 - - - -
573A VAL 3.0 12.6 - - - -
574A GLY* 4.0 4.7 - - - -
587A ALA* 1.3 74.9 - - - +
589A TYR* 1.3 60.5 + - - +
590A THR* 4.2 16.9 - - - +
615A ASN* 3.7 4.4 + - - +
616A TYR* 3.8 2.1 - - - -
617A GLU* 3.0 41.9 + - - +
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Residues in contact with TYR 589 (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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571A PRO* 3.9 31.2 - - + +
572A TYR* 3.8 2.8 - - - -
573A VAL* 2.7 54.5 + - + +
588A SER* 1.3 71.8 - - - +
590A THR* 1.3 68.1 + - - +
591A ASP* 5.2 1.5 + - + -
614A GLN* 3.8 27.9 - - + +
615A ASN 3.5 5.6 - - - -
616A TYR* 3.5 43.7 - + + +
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Residues in contact with THR 590 (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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167A GLN* 4.1 16.8 - - + +
252A ALA* 3.2 22.8 + - - +
571A PRO 4.4 4.9 - - - -
572A TYR* 3.9 27.8 - - + -
573A VAL 5.2 0.2 - - - +
588A SER* 4.2 15.9 - - - +
589A TYR* 1.3 82.2 - - - +
591A ASP* 1.3 61.1 + - - +
614A GLN* 3.2 8.9 - - - +
615A ASN* 2.9 53.2 + - - +
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Residues in contact with ASP 591 (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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252A ALA* 3.7 5.3 - - - +
254A GLY* 2.8 35.0 + - - -
255A LEU 4.3 0.3 + - - -
569A PHE 4.6 1.9 - - - +
570A ILE* 3.7 30.1 - - + +
571A PRO* 3.8 25.5 + - + +
589A TYR* 5.2 2.4 + - + +
590A THR* 1.3 76.3 - - - +
592A ILE* 1.3 73.6 + - - +
593A PHE* 4.6 3.1 - - - -
612A GLU* 4.8 4.3 - - - +
613A GLY 3.0 6.2 - - - +
614A GLN* 3.0 33.6 + - + +
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Residues in contact with ILE 592 (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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216A ASN* 4.1 6.5 - - - +
252A ALA* 4.4 2.7 - - + -
253A THR* 4.2 5.6 - - - +
254A GLY* 3.3 18.8 - - - +
257A THR* 4.3 4.0 - - + -
258A GLY 3.3 26.5 - - - +
260A GLY* 3.3 32.8 - - - +
261A SER 3.5 18.8 - - - +
262A LEU* 3.2 34.3 - - + -
570A ILE* 4.7 3.8 - - + -
591A ASP* 1.3 86.5 - - - +
593A PHE* 1.3 66.1 + - - +
611A ASP 5.7 0.2 - - - +
612A GLU* 3.3 3.9 - - - +
613A GLY 2.9 30.5 + - - +
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Residues in contact with PHE 593 (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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259A ALA* 3.2 16.7 - - + -
260A GLY 2.9 24.4 + - - -
552A VAL* 3.8 22.0 - - + -
554A TYR* 5.4 1.6 - - + -
565A GLU* 4.9 8.3 - - + -
568A ARG* 3.7 42.6 - - + +
569A PHE 5.9 0.2 - - - -
570A ILE* 3.6 35.0 - - + -
591A ASP* 4.6 2.9 - - - -
592A ILE* 1.3 78.0 - - - +
594A MET* 1.3 63.3 + - - +
595A PRO* 4.0 24.5 - - + -
610A PRO* 4.0 14.8 - - + -
611A ASP 3.3 11.0 - - - +
612A GLU* 3.7 20.2 - - + -
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Residues in contact with MET 594 (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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215A ASN* 6.0 3.6 - - + +
226A ALA 5.6 2.2 - - - +
227A ARG* 4.4 21.8 - - + +
259A ALA* 3.8 7.2 - - + +
260A GLY* 3.3 47.6 - - - +
261A SER* 5.1 2.5 - - - -
554A TYR* 3.9 19.7 - - + +
593A PHE* 1.3 76.2 - - - +
595A PRO* 1.4 89.3 - - - +
596A GLN* 3.5 1.6 + - - -
610A PRO* 3.8 2.7 - - - -
611A ASP* 2.8 39.5 + - + +
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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