Contacts of the strand formed by residues 633 - 640 (chain A) in PDB entry 3BMW
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 TRP 633 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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589A VAL* 3.4 5.4 - - - +
590A VAL* 2.9 43.2 + - + -
593A ALA* 2.9 33.1 + - + -
595A THR* 3.5 22.0 - - + -
599A GLU 4.0 3.4 - - - -
600A ASN* 3.5 37.0 - - + -
601A VAL* 3.4 30.5 - - + +
622A MET* 3.5 38.0 - - + +
623A PHE 3.1 5.4 - - - +
624A ASN* 3.2 32.1 - - + -
630A TYR* 3.7 10.3 - + - -
631A PRO 3.3 15.9 + - - -
632A THR* 1.3 76.2 - - - +
634A TYR* 1.3 61.9 + - - +
707A GOL 4.9 2.9 - - - -
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Residues in contact with TYR 634 (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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188A GLU* 2.6 34.8 + - - +
192A TYR* 3.7 27.3 - + - -
587A ARG* 4.4 13.0 - - + -
588A PHE 3.1 12.8 - - - +
589A VAL* 4.2 5.8 - - + -
622A MET* 3.6 3.1 - - - +
623A PHE* 2.8 52.1 + + + +
624A ASN* 4.4 0.2 - - - -
626A VAL* 3.6 4.7 - - - +
627A VAL* 3.1 37.9 + - + +
628A TYR* 3.6 52.7 - + + -
633A TRP* 1.3 75.6 - - - +
635A TYR* 1.3 67.4 + - - +
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Residues in contact with TYR 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187A TYR* 4.3 9.2 - - - -
237A PHE* 6.0 3.1 - + + -
269A ASN* 5.4 1.4 + - - -
586A VAL 3.7 0.7 - - - +
587A ARG* 3.5 0.3 - - - -
588A PHE* 2.9 31.7 + - + -
603A LEU* 6.0 0.4 - - + -
619A ILE* 3.3 32.5 - - + -
620A GLY* 4.0 15.0 + - - -
621A PRO* 3.4 22.6 + - - +
622A MET* 3.7 25.4 - - + -
623A PHE* 3.8 19.0 - + - -
634A TYR* 1.3 84.5 - - - +
636A ASP* 1.3 71.4 + - - +
637A VAL* 3.7 8.7 - - + +
706A GOL 3.2 46.7 - - - -
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Residues in contact with ASP 636 (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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192A TYR* 2.7 23.8 + - - -
204A GLN* 3.8 11.1 - - - +
236A PRO* 3.7 18.9 - - + +
237A PHE* 5.5 0.2 - - - -
238A GLY* 3.2 9.4 - - - -
585A CYS* 3.9 16.2 - - - -
586A VAL 3.6 3.8 - - - -
587A ARG* 2.7 49.4 + - - +
634A TYR* 4.7 0.3 - - - -
635A TYR* 1.3 75.3 + - - +
637A VAL* 1.3 61.0 + - - +
706A GOL 2.7 37.1 + - - +
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Residues in contact with VAL 637 (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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238A GLY* 4.1 3.1 - - - -
584A ILE 3.4 0.7 - - - +
585A CYS* 4.2 3.4 - - - -
586A VAL* 2.8 40.9 + - - +
588A PHE* 3.7 23.6 - - + -
603A LEU* 4.0 5.2 - - + -
609A GLU 4.5 5.6 - - - +
610A LEU* 3.8 28.0 - - + -
619A ILE* 4.0 31.2 - - + -
635A TYR* 3.7 11.9 - - + +
636A ASP* 1.3 79.5 - - - +
638A SER* 1.3 72.4 + - - +
639A VAL* 3.5 5.5 + - + +
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Residues in contact with SER 638 (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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237A PHE* 6.1 0.4 - - - -
238A GLY* 3.4 25.3 - - - -
241A LYS* 3.7 26.1 + - - +
242A ASN* 3.4 8.5 + - - -
583A GLN* 2.7 43.7 + - - +
584A ILE 3.4 5.8 - - - -
609A GLU* 3.4 14.2 - - - +
637A VAL* 1.3 76.4 - - - +
639A VAL* 1.3 64.5 + - - +
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Residues in contact with VAL 639 (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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583A GLN* 3.4 7.3 + - - -
584A ILE* 2.8 33.2 + - - +
586A VAL* 3.5 37.0 - - + -
588A PHE* 4.3 10.1 - - + -
607A VAL* 5.0 1.3 - - + -
609A GLU* 4.2 2.5 - - + -
610A LEU* 3.9 32.3 - - + -
637A VAL* 3.8 8.7 - - + +
638A SER* 1.3 78.1 - - - +
640A PRO* 1.3 74.5 - - + +
645A ILE* 4.9 3.4 - - + -
669A VAL* 3.8 16.8 - - + -
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Residues in contact with PRO 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580A THR* 3.8 31.9 - - + -
581A GLY* 3.9 13.9 - - - +
582A ASN 3.5 6.7 - - - +
583A GLN* 4.0 3.5 - - - +
607A VAL* 4.3 10.3 - - + -
609A GLU* 3.6 20.9 - - + +
639A VAL* 1.3 90.3 - - + +
641A ALA* 1.3 65.9 + - - +
643A THR* 3.2 32.2 + - + +
645A ILE* 5.1 2.5 - - + -
669A VAL* 3.3 16.8 - - - +
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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