Contacts of the helix formed by residues 502 - 510 (chain A) in PDB entry 1CVU
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 GLU 502 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A MET* 3.4 25.5 - - + +
171A LEU* 4.0 5.7 - - + +
452A ILE* 4.0 11.7 - - - +
455A SER* 5.3 4.3 - - - -
456A ARG* 2.6 58.4 + - - +
461A GLN 5.6 0.2 - - - -
463A LEU* 3.8 2.5 - - - +
495A TYR* 2.6 24.1 + - + +
501A MET* 1.3 80.6 - - - +
503A LEU* 1.3 62.6 + - - +
505A PRO* 3.4 16.7 - - + +
506A ALA* 3.0 29.1 + - - +
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Residues in contact with LEU 503 (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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380A GLU* 4.7 9.6 - - + +
383A THR* 4.9 7.2 - - + -
384A LEU* 5.8 1.3 - - + -
460A TYR* 4.3 21.8 - - + -
461A GLN 4.9 4.3 + - - +
462A SER 4.8 0.4 - - - -
463A LEU* 3.9 25.6 - - + +
466A TYR* 3.9 39.9 - - + -
502A GLU* 1.3 70.5 - - - +
504A TYR* 1.3 67.7 + - - +
506A ALA* 3.3 3.1 + - - +
507A LEU* 2.9 39.7 + - + +
521A THR* 4.2 25.4 - - + -
525A LEU* 4.2 16.8 - - + -
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Residues in contact with TYR 504 (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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182A LEU* 4.3 12.6 - - + -
383A THR* 3.8 30.5 - - + +
384A LEU* 5.4 1.1 - - - -
386A HIS* 3.7 32.9 + - + +
388A HIS* 4.3 5.5 - - - +
440A VAL* 5.0 0.3 - - - +
448A ALA* 3.6 25.2 - - - +
451A SER* 3.4 32.9 + - - +
452A ILE* 3.9 17.5 - - + -
455A SER* 4.4 10.5 - - - +
460A TYR* 6.3 0.2 - - - -
502A GLU* 4.7 0.2 - - - +
503A LEU* 1.3 78.0 - - - +
505A PRO* 1.3 73.4 - - + +
507A LEU* 3.1 21.5 + - + +
508A LEU* 3.3 36.7 + - + +
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Residues in contact with PRO 505 (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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177A VAL* 4.1 16.8 - - + -
181A VAL* 6.0 0.4 - - + -
182A LEU* 4.0 17.0 - - + +
452A ILE* 4.5 20.9 - - + -
491A LEU* 5.7 0.4 - - + -
495A TYR* 4.0 9.2 - - - +
501A MET* 3.9 13.9 - - + -
502A GLU* 3.4 33.2 - - + +
504A TYR* 1.3 99.7 - - + +
506A ALA* 1.3 61.1 + - - +
508A LEU* 3.0 14.6 + - + +
509A VAL* 3.1 14.4 + - - +
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Residues in contact with ALA 506 (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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463A LEU* 3.7 33.4 - - + -
481A LEU* 4.1 10.9 - - + +
501A MET* 3.5 15.1 - - + +
502A GLU 3.0 20.0 + - - +
503A LEU 3.4 3.8 - - - +
505A PRO* 1.3 79.2 - - - +
507A LEU* 1.3 56.9 + - - +
509A VAL* 4.6 1.6 - - - +
510A GLU* 2.7 35.6 + - - +
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Residues in contact with LEU 507 (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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384A LEU* 3.6 37.9 - - + +
435A ALA* 3.8 16.1 + - - +
463A LEU* 5.6 0.2 - - - +
503A LEU* 2.9 35.5 + - + +
504A TYR* 3.5 15.3 - - + +
505A PRO 3.1 0.6 - - - -
506A ALA* 1.3 78.7 - - + +
508A LEU* 1.3 63.2 + - + +
509A VAL 3.6 0.3 + - - -
510A GLU* 3.9 12.1 + - - +
519A GLY 5.5 0.5 + - - -
521A THR* 3.6 19.7 - - + +
522A MET* 3.5 56.6 - - + +
525A LEU* 5.6 1.3 - - + -
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Residues in contact with LEU 508 (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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182A LEU* 4.0 15.5 - - + -
386A HIS 4.3 8.1 - - - +
389A PRO* 3.9 12.1 - - + -
434A VAL* 3.4 42.2 - - + +
435A ALA* 4.3 1.6 - - - -
437A GLY* 2.8 26.9 + - - -
440A VAL* 3.5 30.1 - - + -
504A TYR* 3.3 42.4 + - + +
505A PRO 3.0 7.6 + - - +
507A LEU* 1.3 79.9 - - + +
509A VAL* 1.3 59.8 + - - +
522A MET* 4.9 3.1 - - + -
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Residues in contact with VAL 509 (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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181A VAL* 3.6 43.7 - - + +
182A LEU* 4.5 2.5 - - + -
436A GLY 4.2 8.4 - - - +
437A GLY* 3.9 4.9 - - - -
481A LEU* 4.1 9.2 - - + -
482A THR* 3.5 36.1 - - + +
487A MET* 3.9 16.3 - - - +
491A LEU* 3.8 13.5 - - + -
501A MET* 5.1 1.1 - - + -
505A PRO 3.1 13.2 + - - +
506A ALA* 4.1 5.4 - - - +
508A LEU* 1.3 77.6 - - - +
510A GLU* 1.3 70.3 + - - +
511A LYS 3.6 0.9 + - - -
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Residues in contact with GLU 510 (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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435A ALA* 3.6 2.6 - - + +
436A GLY 3.1 19.1 + - - -
463A LEU* 6.3 0.2 - - - -
475A TYR* 2.6 32.0 + - - +
481A LEU* 3.5 18.4 - - + +
506A ALA 2.7 17.6 + - - +
507A LEU* 3.9 12.8 + - - +
508A LEU 3.7 0.6 - - - -
509A VAL* 1.3 78.2 - - - +
511A LYS* 1.3 73.7 + - + +
512A PRO* 3.0 4.2 - - - +
519A GLY* 3.4 20.7 + - - +
520A GLU 3.8 8.8 + - - -
521A THR* 2.9 40.4 + - - -
522A MET* 4.0 2.8 + - - +
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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