Contacts of the strand formed by residues 563 - 578 (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 ILE 563 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227A ARG* 4.1 4.5 - - - +
554A TYR* 3.5 2.8 - - + +
555A ARG* 3.3 4.2 - - - +
556A VAL* 2.8 67.0 + - + +
560A ASN* 5.4 1.8 - - + +
561A PRO 3.5 13.7 - - - +
562A THR* 1.3 74.7 - - - +
564A ARG* 1.3 61.6 + - - +
565A GLU* 5.5 1.6 - - + +
595A PRO* 4.2 20.6 - - + -
596A GLN 4.1 14.6 - - - +
598A SER* 3.9 29.8 - - - +
601A ARG* 6.3 0.7 - - - +
607A LEU* 3.8 28.3 - - + -
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Residues in contact with ARG 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
527A ARG* 3.1 33.9 - - - +
553A ASP* 3.2 30.1 + - - -
554A TYR 3.4 4.9 - - - -
555A ARG* 3.8 39.4 - - + +
562A THR* 4.0 8.2 + - + -
563A ILE* 1.3 75.1 - - - +
565A GLU* 1.3 81.8 + - - +
566A SER* 3.1 27.5 + - - +
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Residues in contact with GLU 565 (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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552A VAL 3.7 2.5 - - - +
553A ASP* 3.4 4.5 - - - -
554A TYR* 3.0 36.7 + - + +
563A ILE* 5.5 2.2 - - + +
564A ARG* 1.3 83.0 - - - +
566A SER* 1.3 62.8 + - - +
568A ARG* 3.4 36.0 + - + +
593A PHE* 4.9 4.5 - - + -
595A PRO* 4.0 25.5 - - + +
607A LEU* 6.1 0.5 - - - +
609A GLU* 5.4 1.4 - - - +
610A PRO* 3.0 32.0 - - + +
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Residues in contact with SER 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553A ASP* 4.5 8.7 - - - -
564A ARG* 3.1 29.1 + - - +
565A GLU* 1.3 75.3 - - - +
567A GLY* 1.3 65.4 + - - +
568A ARG* 3.0 8.8 + - - +
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Residues in contact with GLY 567 (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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551A VAL* 4.2 18.9 - - - +
552A VAL 3.4 9.8 + - - -
553A ASP* 4.5 4.0 - - - +
566A SER* 1.3 71.6 - - - +
568A ARG* 1.3 61.0 + - - +
569A PHE* 3.5 4.5 + - - +
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Residues in contact with ARG 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A ARG 3.6 1.4 - - - +
551A VAL* 3.4 4.5 - - - -
552A VAL* 3.0 36.8 + - - +
565A GLU* 3.4 33.2 + - + +
566A SER 3.0 9.5 + - - +
567A GLY* 1.3 72.8 - - - +
569A PHE* 1.3 65.1 + - - +
570A ILE* 3.8 0.7 + - - +
593A PHE* 3.7 39.9 - - + -
609A GLU* 4.4 9.1 + - - +
610A PRO* 3.5 27.7 - - - +
612A GLU* 3.8 32.3 + - - +
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Residues in contact with PHE 569 (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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548A GLY 4.3 4.7 - - - -
549A GLY* 4.2 22.0 - - - -
550A ARG 3.5 12.1 - - - -
551A VAL* 4.6 12.8 - - + +
567A GLY 3.5 5.3 + - - +
568A ARG* 1.3 77.5 - - - +
570A ILE* 1.3 62.6 + - - +
571A PRO* 3.6 44.7 - - + +
591A ASP* 4.6 2.8 - - - +
593A PHE* 5.7 0.5 - - - -
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Residues in contact with ILE 570 (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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254A GLY* 4.0 32.8 - - - +
255A LEU* 4.2 4.6 - - - +
258A GLY 4.5 8.3 - - - +
549A GLY* 3.0 24.9 - - - -
550A ARG* 2.8 19.1 + - + +
552A VAL* 4.1 15.9 - - + -
568A ARG 4.6 1.8 - - - +
569A PHE* 1.3 77.6 - - - +
571A PRO* 1.3 67.6 - - - +
591A ASP* 3.7 38.8 - - + +
592A ILE* 4.7 2.9 - - - -
593A PHE* 3.6 34.8 - - + -
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Residues in contact with PRO 571 (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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255A LEU* 5.7 0.3 - - - +
548A GLY 3.9 2.2 - - - +
569A PHE* 3.6 33.1 - - + +
570A ILE* 1.3 95.2 - - - +
572A TYR* 1.3 64.4 + - - +
573A VAL* 5.2 4.3 - - + -
589A TYR* 3.9 35.4 - - + +
590A THR* 4.4 0.7 - - - -
591A ASP* 3.8 29.9 + - + -
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Residues in contact with TYR 572 (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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155A ALA* 4.0 3.3 - - - +
156A THR* 3.6 26.4 - - + +
166A PRO* 3.7 17.0 - - + +
167A GLN* 2.3 40.5 + - - +
255A LEU* 3.5 40.8 - - + -
534A THR* 4.7 6.5 - - + -
546A PHE* 4.0 26.7 - + + -
547A LEU* 3.6 4.3 - - - +
548A GLY 2.9 42.9 + - - +
571A PRO* 1.3 78.0 - - - +
573A VAL* 1.3 70.9 + - - +
574A GLY 4.7 3.4 - - - -
588A SER* 5.6 1.6 - - - -
589A TYR 3.8 2.0 - - - -
590A THR* 3.9 18.6 - - + -
591A ASP 6.0 0.2 - - - -
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Residues in contact with VAL 573 (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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545A LEU* 5.3 5.4 - - + -
546A PHE 3.7 2.7 - - - +
547A LEU* 4.2 22.9 - - + -
571A PRO* 5.2 4.3 - - + -
572A TYR* 1.3 86.2 - - - +
574A GLY* 1.3 63.8 + - - +
588A SER* 3.0 5.9 - - - -
589A TYR* 2.7 59.2 + - + +
590A THR* 5.2 0.2 - - - +
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Residues in contact with GLY 574 (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* 4.5 6.7 - - - -
545A LEU* 3.4 8.8 - - - +
546A PHE* 2.7 48.8 + - - +
572A TYR* 4.9 1.3 - - - -
573A VAL* 1.3 77.9 - - - +
575A ALA* 1.3 57.6 + - - -
587A ALA 3.2 10.8 - - - -
588A SER* 4.0 5.6 - - - -
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Residues in contact with ALA 575 (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 2.5 - - - +
543A LEU* 4.4 13.9 - - + -
544A ASN 3.3 11.0 - - - +
545A LEU* 4.1 12.3 - - + -
546A PHE* 4.9 0.9 - - - -
574A GLY* 1.3 75.7 - - - +
576A VAL* 1.3 64.7 + - - +
586A TYR* 3.1 7.6 - - - +
587A ALA* 2.8 38.0 + - + +
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Residues in contact with VAL 576 (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* 4.1 13.5 - - + +
164A GLU* 3.9 26.5 - - + +
166A PRO* 4.0 14.6 - - + -
542A ASP 3.3 5.0 - - - +
543A LEU* 3.5 3.1 - - - -
544A ASN* 3.0 45.7 + - + +
546A PHE* 4.9 3.8 - - + -
575A ALA* 1.3 78.3 - - - +
577A TYR* 1.3 61.6 + - - +
578A ASP* 4.1 8.5 - - - +
584A SER* 4.0 19.1 - - - -
585A VAL 3.4 7.4 - - - +
586A TYR* 3.7 14.4 - - + -
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Residues in contact with TYR 577 (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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540A THR* 5.2 1.3 - - - -
542A ASP* 3.3 33.7 + - + -
543A LEU* 4.0 23.3 - - + -
575A ALA 4.3 0.4 - - - -
576A VAL* 1.3 72.7 - - - +
578A ASP* 1.3 74.0 + - - +
579A LEU* 4.0 20.7 - - + +
584A SER* 3.1 1.7 - - - -
585A VAL* 2.6 55.0 + - + +
586A TYR* 4.8 0.2 - - - +
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Residues in contact with ASP 578 (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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127A LEU* 3.7 26.6 - - + +
128A GLY* 3.9 9.6 + - - -
163A ARG* 4.5 7.5 + - - +
541A ASP 3.8 5.4 - - - +
542A ASP* 2.9 51.2 + - + +
544A ASN* 4.9 4.1 + - - -
576A VAL* 4.1 10.2 - - - +
577A TYR* 1.3 84.5 - - - +
579A LEU* 1.3 62.0 + - - +
580A ASN 4.6 3.8 - - - +
583A TYR 4.5 1.1 - - - +
584A SER* 2.8 27.2 + - - +
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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
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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