Contacts of the strand formed by residues 591 - 600 (chain A) in PDB entry 3W5D
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 591 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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514A VAL* 3.7 38.1 - - + -
521A VAL* 4.2 16.6 - - + +
524A ARG* 2.9 22.2 + - + +
525A CYS* 3.4 9.3 - - - -
526A ASN 2.9 22.7 + - - -
527A TYR* 3.2 7.8 + - - -
565A ALA* 4.1 13.0 - - + -
566A THR 3.7 3.1 - - - +
567A ARG* 3.6 33.4 - - + +
588A GLU* 3.8 27.1 - - - +
589A THR 3.8 2.9 - - - +
590A ASP* 1.3 80.5 - - - +
592A THR* 1.3 63.8 + - - +
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Residues in contact with THR 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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525A CYS* 3.9 0.2 - - - -
527A TYR* 3.2 27.3 - - + +
528A VAL 3.9 2.9 - - - -
529A ARG* 3.5 51.4 - - + +
534A ARG* 4.1 3.3 + - + -
565A ALA* 3.1 5.5 - - - +
566A THR 2.7 42.0 + - - -
568A ASP* 2.8 23.0 + - - +
591A LEU* 1.3 71.4 - - - +
593A PHE* 1.3 65.6 + - - +
594A VAL* 3.3 1.7 + - - +
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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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367A PHE* 3.9 11.4 - + - -
369A ILE* 3.7 26.9 - - + -
521A VAL* 5.7 0.2 - - + -
522A ILE* 4.3 18.4 - - + -
525A CYS* 3.4 20.0 - - - -
527A TYR 2.7 14.8 + - - +
528A VAL* 4.4 3.4 - - + -
529A ARG* 2.8 30.1 + - - +
537A MET* 4.0 10.8 - - + -
545A ILE* 3.6 33.2 - - + -
563A ALA* 4.5 5.4 - - + -
564A LEU 3.8 7.4 - - - -
565A ALA* 5.4 0.2 - - + -
592A THR* 1.3 69.8 - - - +
594A VAL* 1.3 62.8 + - - +
595A GLY* 3.3 42.4 - - - -
596A VAL* 3.7 17.9 - - + -
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Residues in contact with VAL 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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368A ILE* 3.6 20.8 - - - +
369A ILE* 4.3 3.1 + - - +
409A GLY* 3.8 12.9 - - - +
412A GLU* 3.3 26.0 - - + +
413A LEU* 3.7 33.4 - - + +
416A ILE* 4.0 7.0 - - + -
529A ARG* 4.4 14.0 - - + +
564A LEU 2.9 15.1 + - - +
566A THR* 3.4 28.5 - - + +
592A THR 3.3 7.8 + - - +
593A PHE* 1.3 81.6 - - - +
595A GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 595 (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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367A PHE 3.2 13.0 - - - -
413A LEU* 3.8 15.4 - - - +
564A LEU* 2.7 35.0 + - - -
593A PHE* 3.3 16.0 - - - -
594A VAL* 1.3 83.3 - - - +
596A VAL* 1.3 62.5 + - - +
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Residues in contact with VAL 596 (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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366A MET* 2.9 26.0 - - - +
367A PHE* 2.9 49.1 + - + +
413A LEU* 4.1 1.7 - - - +
549A ILE* 4.0 26.7 - - + -
552A TRP* 4.4 7.2 - - + -
561A CYS* 4.2 11.0 - - + -
562A LEU 3.3 14.1 - - - +
563A ALA* 4.3 5.2 - - + -
564A LEU* 5.1 0.2 - - - -
593A PHE* 3.7 13.0 - - + -
595A GLY* 1.3 79.1 - - - +
597A VAL* 1.3 77.0 + - - +
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Residues in contact with VAL 597 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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363A VAL* 4.0 17.0 - - + -
365A LYS 3.5 3.8 - - - -
366A MET* 4.0 7.2 - - + -
413A LEU* 3.9 26.7 - - + -
417A CYS* 4.3 1.3 - - - -
445A LEU* 4.1 24.0 - - + -
448A LEU* 4.1 11.7 - - + -
560A ARG 3.9 0.9 - - - +
561A CYS* 3.5 2.3 - - - -
562A LEU* 3.0 48.0 + - + +
564A LEU* 4.0 13.7 - - + -
596A VAL* 1.3 82.1 - - - +
598A GLY* 1.3 59.7 + - - +
599A MET* 4.9 3.6 - - + -
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Residues in contact with GLY 598 (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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363A VAL* 3.4 3.4 - - - -
364A CYS* 2.8 26.0 + - - -
365A LYS 3.0 15.0 + - - +
552A TRP* 4.1 15.4 - - - -
559A LEU* 4.1 18.5 - - - +
560A ARG 3.6 5.8 - - - -
561A CYS* 4.4 3.1 - - - -
597A VAL* 1.3 72.3 - - - +
599A MET* 1.3 60.8 + - - -
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Residues in contact with MET 599 (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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361A MET* 3.3 36.6 - - + -
362A SER 3.0 15.9 - - - +
363A VAL* 4.0 6.3 - - + -
441A THR* 3.2 44.9 - - + +
444A ALA* 3.7 9.9 - - + -
445A LEU* 3.4 22.9 - - + -
558A THR 4.4 0.2 - - - +
559A LEU* 3.2 12.1 - - - +
560A ARG* 2.9 46.9 + - + +
562A LEU* 4.7 6.1 - - + -
597A VAL* 4.1 4.2 - - + +
598A GLY* 1.3 72.7 - - - +
600A LEU* 1.3 60.0 + - - +
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Residues in contact with LEU 600 (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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361A MET* 3.4 10.3 - - - -
362A SER* 2.7 32.5 + - - +
364A CYS* 3.8 16.6 - - - -
557A ASP 3.7 12.3 - - - +
558A THR* 3.5 31.6 - - - +
559A LEU* 3.7 10.3 - - + -
599A MET* 1.3 74.9 - - - +
601A ASP* 1.3 73.9 + - - +
602A PRO* 3.5 23.5 - - + +
603A PRO* 5.0 0.9 - - + -
638A ARG* 3.7 26.0 - - - +
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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