Contacts of the strand formed by residues 611 - 624 (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 ASP 611 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A GLY 5.0 0.7 - - - +
262A LEU* 4.9 3.6 - - - +
592A ILE* 5.7 0.7 - - - +
593A PHE* 3.3 2.6 - - - -
594A MET* 2.8 40.6 + - + +
596A GLN* 3.4 20.8 - - + +
610A PRO* 1.3 68.3 - - - +
612A GLU* 1.3 59.6 + - - +
640A GLU* 2.4 35.6 - - - +
641A GLU 3.7 5.5 - - - +
642A ASN 3.7 10.9 - - - +
643A ARG* 4.0 7.3 - - - +
644A ALA* 4.6 1.4 + - - +
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Residues in contact with GLU 612 (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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262A LEU* 4.1 5.2 - - - -
568A ARG* 3.8 21.8 + - - +
591A ASP* 4.8 4.5 - - - +
592A ILE 3.3 9.0 - - - +
593A PHE* 3.7 19.3 - - + +
609A GLU* 5.5 0.5 - - - +
610A PRO* 3.1 7.1 + - - +
611A ASP* 1.3 72.4 - - - +
613A GLY* 1.3 59.0 + - - +
614A GLN* 4.2 6.5 + - - +
640A GLU* 3.3 10.4 - - - +
641A GLU* 2.9 51.9 + - - +
642A ASN* 3.2 24.3 + - - -
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Residues in contact with GLY 613 (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* 4.2 0.5 - - - +
262A LEU* 3.5 27.1 - - - +
591A ASP* 3.0 16.8 - - - +
592A ILE 2.9 20.5 + - - -
612A GLU* 1.3 77.2 - - - +
614A GLN* 1.3 65.6 + - - -
639A HIS 3.0 11.9 - - - -
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Residues in contact with GLN 614 (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* 4.7 0.7 - - - -
589A TYR* 3.8 34.1 - - + +
590A THR 3.2 8.7 - - - +
591A ASP* 3.0 25.5 + - - +
612A GLU* 4.2 6.5 + - - +
613A GLY* 1.3 81.2 - - - +
615A ASN* 1.3 59.3 + - - +
616A TYR* 4.0 15.3 + - + +
637A GLU 3.6 1.9 - - - +
638A ILE* 3.4 6.3 - - - +
639A HIS* 2.8 43.0 + - - +
641A GLU* 2.6 40.2 + - - +
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Residues in contact with ASN 615 (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* 6.4 0.2 - - - +
210A ARG* 3.2 13.3 + - - -
251A GLY* 3.2 22.4 - - - -
252A ALA* 3.7 15.7 - - + +
588A SER* 3.7 3.4 + - - +
589A TYR* 3.5 6.9 - - - -
590A THR* 2.9 45.3 + - - +
614A GLN* 1.3 71.9 - - - +
616A TYR* 1.3 67.6 + - - +
617A GLU* 3.3 33.4 + - - +
636A PHE* 4.1 2.7 - - - +
637A GLU 3.5 4.7 - - - -
638A ILE* 3.6 18.2 - - + +
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Residues in contact with TYR 616 (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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588A SER 3.8 2.7 - - - -
589A TYR* 3.5 39.7 - + + -
614A GLN* 4.1 17.8 + - + +
615A ASN* 1.3 73.8 + - - +
617A GLU* 1.3 61.5 + - - +
635A TYR* 3.9 0.7 - - - +
636A PHE* 3.2 5.0 - - - -
637A GLU* 2.8 50.2 + - + +
639A HIS* 4.0 37.3 + + + -
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Residues in contact with GLU 617 (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* 4.6 5.1 - - - +
168A SER* 2.5 39.1 + - - -
210A ARG* 3.0 25.1 + - - -
250A LYS 4.3 2.4 - - - +
586A TYR* 2.8 31.7 + - + +
587A ALA* 3.2 6.9 - - - +
588A SER* 3.0 41.4 + - - +
615A ASN* 3.3 14.3 + - - +
616A TYR* 1.3 76.7 - - - +
618A ILE* 1.3 65.2 + - - +
634A ALA* 3.6 6.9 - - + +
635A TYR 3.4 10.3 - - - +
636A PHE* 4.5 1.8 - - + -
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Residues in contact with ILE 618 (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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585A VAL* 6.0 6.5 - - + -
586A TYR 3.4 12.1 - - - +
587A ALA* 4.2 12.8 - - + -
617A GLU* 1.3 76.1 - - - +
619A GLY* 1.3 61.9 - - - +
634A ALA* 3.7 1.7 - - - +
635A TYR* 2.9 50.6 + - + +
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Residues in contact with GLY 619 (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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585A VAL* 3.1 9.9 - - - +
586A TYR* 2.8 55.4 + - - -
618A ILE* 1.3 79.6 - - - +
620A ILE* 1.3 60.1 + - - -
633A LEU 3.5 9.9 - - - -
634A ALA* 4.2 0.2 - - - -
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Residues in contact with ILE 620 (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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579A LEU* 5.0 7.0 - - + -
583A TYR* 3.7 34.8 - - + -
584A SER 3.3 13.5 - - - +
585A VAL* 4.1 14.4 - - + -
586A TYR* 3.8 0.6 - - - -
619A GLY* 1.3 74.2 - - - +
621A LYS* 1.3 67.1 + - - +
632A SER* 3.3 2.9 - - - -
633A LEU* 2.9 61.7 + - + +
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Residues in contact with LYS 621 (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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162A PRO* 2.8 29.5 + - - +
163A ARG* 4.1 22.8 + - + +
165A THR* 2.5 33.1 + - - +
167A GLN 3.0 16.9 + - - -
168A SER* 5.4 2.0 - - - +
169A ILE* 4.2 7.8 - - - +
582A THR 4.0 0.5 - - - +
583A TYR* 3.5 5.1 - - - -
584A SER* 2.9 35.2 + - - +
586A TYR* 3.8 28.7 - - + -
620A ILE* 1.3 80.0 - - - +
622A GLY* 1.3 60.1 + - - +
631A THR 3.1 5.4 - - - +
632A SER* 3.7 19.5 - - - -
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Residues in contact with GLY 622 (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* 5.4 1.6 - - - -
582A THR* 3.2 10.1 - - - -
583A TYR* 3.7 15.1 - - - -
621A LYS* 1.3 74.6 - - - +
623A GLU* 1.3 60.6 + - - -
624A TYR* 3.6 4.3 - - - -
630A ASN* 3.4 6.3 + - - +
631A THR* 2.6 51.9 + - - +
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Residues in contact with GLU 623 (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* 6.0 1.2 - - - +
161A THR* 4.2 13.3 + - - +
163A ARG* 3.4 52.1 + - + +
581A ASP 4.6 2.4 - - - +
582A THR* 3.0 23.6 + - - +
622A GLY* 1.3 75.1 - - - -
624A TYR* 1.3 67.5 + - - +
626A ASP* 5.3 0.7 - - - -
627A GLY* 3.9 27.2 + - - +
629A LEU 3.6 2.9 - - - +
630A ASN* 4.0 15.2 + - - +
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Residues in contact with TYR 624 (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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582A THR* 3.6 28.3 - - + -
583A TYR* 2.8 28.1 + + - -
622A GLY 3.6 8.5 - - - -
623A GLU* 1.3 72.6 - - - +
625A LEU* 1.3 74.0 - - + +
626A ASP 3.3 3.1 - - - -
627A GLY 3.0 11.1 + - - -
629A LEU* 2.7 64.3 + - + +
631A THR* 2.8 44.2 + - + +
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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