Contacts of the strand formed by residues 444 - 450 (chain A) in PDB entry 2V3D
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 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A LEU* 3.8 26.5 - - + -
67A LEU* 5.2 4.7 - - + -
442A ASN* 3.0 19.7 + - - +
443A ASP* 1.3 83.1 - - + +
445A ASP* 1.3 66.3 + - - +
446A ALA* 4.0 5.4 + - + +
460A VAL* 4.0 20.9 - - + -
461A LEU 3.5 5.4 - - - +
462A ASN* 3.5 43.5 - - + +
468A VAL* 4.2 15.9 - - + -
470A LEU* 4.2 19.7 - - + -
484A SER* 3.7 6.3 - - - +
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Residues in contact with ASP 445 (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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365A HIS* 2.7 38.8 + - - -
368A ILE* 3.8 32.6 - - + +
369A THR* 5.1 1.6 + - - -
372A LEU* 5.9 1.1 - - - -
443A ASP 4.0 2.7 + - - +
444A LEU* 1.3 76.7 - - - +
446A ALA* 1.3 59.2 + - - +
460A VAL* 3.5 2.4 - - - +
461A LEU* 2.7 50.8 + - + +
463A ARG* 3.5 17.4 + - - +
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Residues in contact with ALA 446 (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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67A LEU* 3.9 21.3 - - + -
368A ILE* 3.8 4.7 - - - +
372A LEU* 3.8 21.1 - - - +
436A LEU* 3.9 21.5 - - + +
444A LEU* 4.0 5.9 + - + +
445A ASP* 1.3 77.1 - - - +
447A VAL* 1.3 63.1 + - - +
459A VAL 3.2 10.5 - - - +
460A VAL* 4.3 9.6 - - + -
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Residues in contact with VAL 447 (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* 4.1 22.4 - - + -
371A LEU* 3.9 40.4 - - + -
372A LEU* 3.9 16.4 - - + -
423A PHE* 4.3 1.3 - - + -
433A ARG* 3.9 21.3 - - + -
436A LEU* 4.1 5.6 - - - -
446A ALA* 1.3 75.6 - - - +
448A ALA* 1.3 63.1 + - - +
449A LEU* 4.1 13.3 - - + +
457A VAL 4.0 0.3 - - - +
458A VAL* 3.3 4.0 - - - +
459A VAL* 3.0 41.2 + - + +
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Residues in contact with ALA 448 (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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69A LEU* 3.5 31.0 - - + -
372A LEU* 5.6 0.2 - - - +
433A ARG* 3.6 4.2 - - - +
434A VAL* 3.0 31.3 + - + +
435A GLY 4.1 0.7 - - - +
436A LEU* 3.9 23.6 - - + +
447A VAL* 1.3 75.3 - - - +
449A LEU* 1.3 67.7 + - - +
457A VAL 3.4 5.2 - - - -
458A VAL* 3.9 9.9 - - + -
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Residues in contact with LEU 449 (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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69A LEU* 5.4 0.7 - - - +
78A VAL* 3.7 30.3 - - + -
371A LEU* 4.6 10.5 - - + -
427A ILE* 3.9 34.5 - - + -
431A SER* 4.7 7.4 - - - -
432A GLN 3.3 9.2 - - - +
433A ARG* 3.9 20.9 - - + +
434A VAL* 4.1 4.3 - - - +
447A VAL* 4.1 24.0 - - + +
448A ALA* 1.3 82.6 - - - +
450A MET* 1.3 65.3 + - - +
456A ALA* 3.6 5.0 - - - +
457A VAL* 2.8 46.4 + - + +
459A VAL* 5.4 1.3 - - + -
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Residues in contact with MET 450 (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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69A LEU* 5.3 2.0 - - + -
71A PRO* 3.9 24.9 - - - -
74A LYS* 3.5 28.9 - - - +
430A GLY 4.6 0.2 - - - +
431A SER* 3.2 4.3 - - - -
432A GLN* 2.8 40.0 + - + +
434A VAL* 4.0 15.3 - - + -
449A LEU* 1.3 78.5 - - - +
451A HIS* 1.3 66.6 + - - +
454A GLY* 3.9 24.7 - - - +
455A SER 3.3 10.8 - - - +
456A ALA* 4.7 3.1 - - + -
496A ARG* 4.3 19.7 - - - +
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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