Contacts of the strand formed by residues 444 - 450 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65B LEU* 3.9 24.7 - - + -
67B LEU* 5.2 4.0 - - + -
442B ASN* 3.0 20.7 + - - +
443B ASP* 1.3 82.7 - - + +
445B ASP* 1.3 66.5 + - - +
446B ALA* 4.0 4.4 + - + +
460B VAL* 3.8 23.8 - - + -
461B LEU 3.4 4.5 - - - +
462B ASN* 3.5 45.3 - - + +
468B VAL* 4.1 22.0 - - + -
470B LEU* 4.4 9.0 - - + -
484B SER* 3.7 10.8 - - - +
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Residues in contact with ASP 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B HIS* 2.8 36.7 + - - -
368B ILE* 3.7 31.6 - - + +
369B THR* 5.3 1.2 + - - -
372B LEU* 6.1 0.4 - - - -
443B ASP 4.1 2.4 + - - +
444B LEU* 1.3 76.5 - - - +
446B ALA* 1.3 61.3 + - - +
460B VAL* 3.5 2.9 - - - +
461B LEU* 2.7 46.7 + - + +
463B ARG* 3.3 24.4 + - - -
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Residues in contact with ALA 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B LEU* 3.9 20.9 - - + -
368B ILE* 3.9 5.1 - - - +
372B LEU* 3.7 22.6 - - - +
436B LEU* 3.7 22.1 - - + +
444B LEU* 4.0 4.9 + - + -
445B ASP* 1.3 76.0 - - - +
447B VAL* 1.3 65.0 + - - +
458B VAL* 5.0 0.2 - - + -
459B VAL 3.2 10.8 - - - +
460B VAL* 4.4 8.7 - - + -
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Residues in contact with VAL 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B ILE* 4.1 21.8 - - + +
371B LEU* 3.9 27.4 - - + -
372B LEU* 3.8 13.9 - - + -
423B PHE* 4.3 1.3 - - + -
433B ARG* 3.8 33.0 - - + -
436B LEU* 4.1 5.8 - - - -
446B ALA* 1.3 77.8 - - - +
448B ALA* 1.3 62.7 + - - +
449B LEU* 4.1 16.1 - - + +
457B VAL 3.9 0.9 - - - +
458B VAL* 3.3 4.2 - - - +
459B VAL* 3.0 40.0 + - + -
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Residues in contact with ALA 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 3.3 33.7 - - + -
433B ARG* 3.7 3.8 - - - +
434B VAL* 3.0 31.3 + - + +
435B GLY 4.2 0.2 - - - +
436B LEU* 3.9 27.3 - - + +
447B VAL* 1.3 74.9 - - - +
449B LEU* 1.3 66.2 + - - +
457B VAL 3.3 4.3 - - - -
458B VAL* 4.0 6.3 - - + -
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Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 5.5 0.2 - - - +
78B VAL* 3.6 30.5 - - + -
371B LEU* 4.5 8.3 - - + -
427B ILE* 3.6 35.9 - - + -
431B SER* 4.6 4.5 - - - -
432B GLN 3.3 8.3 - - - +
433B ARG* 3.9 24.2 - - + +
434B VAL 4.2 0.9 - - - +
447B VAL* 4.1 22.9 - - + +
448B ALA* 1.3 81.0 - - - +
450B MET* 1.3 70.1 + - - +
456B ALA* 3.6 3.6 - - - +
457B VAL* 2.7 49.6 + - + +
459B VAL* 5.4 0.9 - - + -
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Residues in contact with MET 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B LEU* 3.8 21.8 - - + -
71B PRO* 4.2 9.6 - - + -
74B LYS* 5.5 7.9 - - - +
430B GLY 4.7 0.3 - - - +
431B SER* 3.3 4.1 - - - -
432B GLN* 2.7 46.2 + - + +
434B VAL* 3.5 40.2 - - + -
449B LEU* 1.3 76.4 - - - +
451B HIS* 1.3 66.0 + - - +
454B GLY* 3.7 21.5 - - - +
455B SER 3.5 15.0 - - - +
456B ALA* 3.9 4.9 - - + -
496B ARG* 3.7 20.4 - - - +
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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