Contacts of the helix formed by residues 505 - 510 (chain B) in PDB entry 3FVO
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 THR 505 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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768A LEU* 4.0 6.1 - - - -
772A GLU* 3.3 7.0 - - - -
503B THR* 3.4 19.5 + - + +
504B ILE* 1.3 79.3 - - - +
506B TYR* 1.3 53.2 + - - +
507B VAL* 3.5 6.6 - - - +
508B ARG* 3.2 28.2 + - - +
509B GLU* 2.8 35.9 + - - +
514B PHE* 4.0 2.6 - - - -
674B SER* 4.0 9.0 - - - -
968B GOL 3.4 43.7 - - - +
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Residues in contact with TYR 506 (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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459A ILE* 6.3 0.2 - - + -
765A ILE* 3.4 43.5 - - + +
768A LEU* 4.0 17.2 - - + +
769A GLN* 3.7 37.9 + - + +
772A GLU* 2.8 29.8 + - - +
505B THR* 1.3 70.1 - - - +
507B VAL* 1.3 77.7 + - + +
509B GLU* 3.2 11.2 + - - +
510B LYS* 3.0 51.1 + - + +
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Residues in contact with VAL 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
772A GLU* 5.0 1.5 + - - +
477B GLN* 5.2 4.0 - - - +
483B TRP* 3.8 30.3 - - + -
505B THR* 3.5 11.4 - - - +
506B TYR* 1.3 95.5 - - + +
508B ARG* 1.3 65.5 + - + +
510B LYS* 3.6 21.8 + - - +
511B VAL* 3.9 4.3 - - - +
677B THR* 4.3 12.6 - - + -
681B LYS* 3.4 32.3 - - + +
968B GOL 3.8 14.4 - - - +
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Residues in contact with ARG 508 (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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2B 8EP 2.8 43.8 + - - -
474B TYR* 3.8 2.2 - - - +
475B GLY 2.9 39.2 + - - +
483B TRP* 3.7 19.0 - - + -
487B VAL* 3.7 13.2 - - + +
502B LEU* 3.6 11.8 - - - +
503B THR* 3.0 27.5 + - - +
505B THR* 3.2 19.6 + - - +
507B VAL* 1.3 74.3 - - + +
509B GLU* 1.3 61.1 + - - +
510B LYS 3.1 2.5 - - - -
511B VAL* 2.9 24.4 + - - +
512B ILE* 2.9 22.6 + - + +
514B PHE* 3.6 17.5 - - + -
674B SER* 3.8 14.3 - - - +
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Residues in contact with GLU 509 (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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516A LYS* 2.7 37.2 + - - +
764A THR* 3.5 11.2 - - + +
765A ILE* 3.7 27.5 - - + +
768A LEU* 3.6 17.4 - - + +
505B THR 2.8 18.3 + - - +
506B TYR 3.2 4.0 + - - +
508B ARG* 1.3 76.6 - - - +
510B LYS* 1.3 58.6 + - - +
512B ILE 3.0 37.4 - - - +
513B ASP* 3.6 7.1 - - - +
514B PHE* 3.2 25.5 + - + +
755B ILE* 5.0 1.7 - - - +
760B ARG* 4.4 3.7 + - - -
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Residues in contact with LYS 510 (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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765A ILE* 3.9 26.9 - - + -
506B TYR* 3.0 57.3 + - + +
507B VAL* 3.8 17.4 - - - +
508B ARG 3.1 0.8 - - - -
509B GLU* 1.3 78.1 - - - +
511B VAL* 1.3 64.2 + - + +
755B ILE* 3.5 13.9 - - - +
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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