Contacts of the helix formed by residues 374 - 383 (chain C) in PDB entry 5V3M
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 374 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362C PRO 3.6 4.2 - - - -
373C HIS* 1.3 80.3 - - - +
375C PRO* 1.3 69.3 - - - +
376C SER* 4.2 6.1 - - - -
377C GLN* 3.6 24.4 - - - +
378C LEU* 2.9 28.9 + - - +
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Residues in contact with PRO 375 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C PRO* 3.5 30.9 - - + -
374C THR* 1.3 86.7 - - - +
376C SER* 1.3 59.7 + - - +
378C LEU* 3.7 9.5 - - + +
379C SER* 2.9 25.1 + - - -
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Residues in contact with SER 376 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
374C THR* 4.4 7.3 - - - -
375C PRO* 1.3 78.5 - - - +
377C GLN* 1.3 59.3 + - - +
378C LEU 3.2 1.6 - - - -
379C SER* 3.5 7.2 + - - -
380C HIS* 3.1 27.0 + - - +
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Residues in contact with GLN 377 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372C PHE* 3.8 7.9 - - + +
373C HIS 4.9 3.8 - - - +
374C THR* 3.2 28.3 + - - +
376C SER* 1.3 78.2 + - - +
378C LEU* 1.3 57.8 + - - +
380C HIS* 4.0 6.9 - - - +
381C HIS* 3.3 22.0 + - - +
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Residues in contact with LEU 378 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362C PRO 4.9 4.3 - - - -
363C HIS* 4.0 28.0 - - + +
364C LYS 4.7 2.0 - - - +
365C CYS* 4.5 19.7 - - - +
372C PHE* 3.9 20.9 - - + +
374C THR 2.9 17.1 + - - +
375C PRO* 3.7 8.3 - - + +
377C GLN* 1.3 74.3 - - - +
379C SER* 1.3 58.6 + - - +
380C HIS 3.2 1.1 - - - -
381C HIS* 2.7 33.2 + - + +
382C GLN* 3.0 42.6 + - + +
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Residues in contact with SER 379 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C PRO 2.9 17.1 + - - -
376C SER* 3.5 10.6 + - - -
378C LEU* 1.3 79.2 - - - +
380C HIS* 1.3 60.8 + - - +
381C HIS 3.3 0.5 + - - -
382C GLN* 3.2 26.5 + - - +
383C LYS* 3.4 11.4 + - - +
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Residues in contact with HIS 380 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C SER 3.1 22.0 + - - +
377C GLN* 4.0 8.7 - - - +
378C LEU 3.2 0.2 - - - -
379C SER* 1.3 75.7 + - - +
381C HIS* 1.3 62.0 + - - +
383C LYS* 3.6 16.8 - - - +
384C LEU* 4.0 9.2 - - - +
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Residues in contact with HIS 381 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C CYS* 3.0 21.1 - - + +
368C CYS* 3.1 9.6 - - - -
370C LYS* 4.9 6.6 - - + +
372C PHE* 4.5 10.3 - - + -
377C GLN 3.3 13.6 + - - +
378C LEU* 2.7 24.2 + - + +
380C HIS* 1.3 76.3 - - - +
382C GLN* 1.3 72.0 + - + -
384C LEU* 3.2 35.4 + - + +
385C HIS* 3.4 10.7 + + - -
1001C ZN 2.0 38.4 - - - -
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Residues in contact with GLN 382 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365C CYS* 5.1 6.1 - - + -
378C LEU* 3.0 42.3 + - + +
379C SER* 3.2 23.7 + - - +
381C HIS* 1.3 87.3 - - + +
383C LYS* 1.3 65.5 + - - +
384C LEU 3.1 1.8 - - - -
385C HIS* 3.2 23.5 + - + +
386C VAL* 4.0 10.6 - - - +
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Residues in contact with LYS 383 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379C SER 3.4 9.5 + - - +
380C HIS* 3.6 15.3 - - - +
381C HIS 3.2 0.8 - - - -
382C GLN* 1.3 78.6 - - - +
384C LEU* 1.3 64.8 + - + +
385C HIS 3.2 1.0 + - - -
386C VAL* 3.4 16.4 + - - +
534C LYS* 3.3 19.9 - - + +
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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