Contacts of the helix formed by residues 402 - 411 (chain A) in PDB entry 2V4M
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 402 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A ALA 2.9 18.3 + - - +
399A GLY* 3.5 4.5 + - - -
400A VAL 3.1 0.4 - - - -
401A ALA* 1.3 82.3 - - - +
403A ARG* 1.3 66.9 + - - +
404A GLN 3.2 2.9 - - - -
405A VAL* 3.5 12.0 + - + +
406A LEU* 3.1 29.8 + - - +
500A PHE* 3.7 40.2 - - + +
503A LEU* 3.3 30.8 - - + +
504A VAL* 4.2 8.1 - - + -
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Residues in contact with ARG 403 (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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399A GLY 3.0 14.8 + - - +
400A VAL* 3.5 12.0 + - - +
402A THR* 1.3 79.3 - - - +
404A GLN* 1.3 56.6 + - - +
406A LEU* 3.4 3.1 + - - +
407A GLU* 3.0 42.5 + - - +
414A VAL* 2.9 38.4 + - + +
415A MET* 4.7 4.2 - - - +
416A VAL* 3.9 22.6 - - + +
415B MET* 3.7 12.1 - - - +
417B GLU* 2.7 30.1 + - - -
421B ASP* 4.3 4.2 + - - -
425B ARG* 2.9 46.6 - - - +
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Residues in contact with GLN 404 (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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400A VAL 4.9 1.0 + - - -
401A ALA 5.4 0.4 - - - -
402A THR 3.2 0.6 - - - -
403A ARG* 1.3 77.7 - - - +
405A VAL* 1.3 61.0 + - - +
407A GLU* 3.4 12.1 + - - +
408A GLU* 2.9 30.2 + - + +
564A GLY* 4.4 5.0 - - - -
565A TYR* 3.6 54.0 + - + +
615A HIS* 3.5 15.9 + - - -
424B ASP 3.1 26.8 + - - +
425B ARG* 3.8 34.5 + - + +
426B ASN* 5.4 2.0 - - - +
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Residues in contact with VAL 405 (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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402A THR* 3.5 20.5 + - + +
404A GLN* 1.3 79.8 - - - +
406A LEU* 1.3 57.4 + - + +
408A GLU* 4.2 14.1 - - - +
409A LEU* 2.8 59.5 + - + +
504A VAL* 4.5 21.3 - - + -
507A ALA* 4.5 10.5 - - + -
524A ILE* 4.2 4.3 - - + -
565A TYR* 4.6 2.5 - - + -
661A CYS* 4.0 37.9 - - + +
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Residues in contact with LEU 406 (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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387A LEU* 4.1 9.4 - - + -
389A LEU* 4.1 16.2 - - + -
402A THR* 3.1 41.6 + - - +
403A ARG* 3.7 4.7 - - - +
405A VAL* 1.3 74.1 - - + +
407A GLU* 1.3 54.3 + - - +
410A THR* 2.5 44.5 + - + +
414A VAL* 3.9 15.5 - - + -
503A LEU* 3.7 25.8 - - + +
506A PHE* 3.6 34.5 - - + -
507A ALA* 3.7 18.4 - - + -
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Residues in contact with GLU 407 (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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403A ARG* 3.0 35.4 + - - +
404A GLN* 3.4 14.6 - - - +
406A LEU* 1.3 76.2 - - - +
408A GLU* 1.3 57.7 + - - +
411A GLU* 2.8 30.3 + - - +
412A LEU 3.9 11.2 - - - +
413A PRO* 5.7 0.2 - - - +
414A VAL* 3.7 18.9 + - + +
425B ARG* 2.7 49.1 + - - +
426B ASN 5.4 0.2 - - - +
427B THR* 4.1 4.8 + - - +
428B PRO* 3.7 31.7 - - + +
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Residues in contact with GLU 408 (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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404A GLN* 2.9 19.9 + - + +
405A VAL* 3.7 8.3 - - - +
406A LEU 3.3 0.2 - - - -
407A GLU* 1.3 79.5 - - - +
409A LEU* 1.3 71.0 + - + +
411A GLU* 3.6 7.3 - - - +
517A MET* 3.3 20.1 - - + +
520A ARG* 2.7 55.3 + - - +
565A TYR* 4.0 7.3 + - - -
425B ARG 5.7 2.4 + - - +
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Residues in contact with LEU 409 (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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405A VAL* 2.8 43.5 + - + +
408A GLU* 1.3 82.0 - - + +
410A THR* 1.3 59.2 + - - +
411A GLU* 4.6 0.3 - - - +
504A VAL* 6.2 0.4 - - + -
507A ALA* 3.6 37.5 - - + +
508A LEU* 4.0 8.5 - - + -
510A MET 4.6 0.9 - - - +
511A CYS* 3.3 40.7 + - - +
514A ARG* 5.5 0.7 - - - +
517A MET* 3.8 21.7 - - + +
520A ARG* 4.1 24.9 - - + -
521A ARG 5.6 1.1 - - - +
524A ILE* 3.8 15.5 - - + -
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Residues in contact with THR 410 (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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387A LEU* 4.3 15.3 - - + +
406A LEU* 2.5 41.8 + - + +
409A LEU* 1.3 72.4 - - - +
411A GLU* 1.3 68.8 + - - +
412A LEU* 3.0 42.7 + - - +
414A VAL* 4.5 2.6 - - - +
507A ALA* 4.9 2.5 - - - -
510A MET* 3.9 37.5 - - + +
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Residues in contact with GLU 411 (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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385A ARG* 5.3 0.7 + - - -
407A GLU 2.8 17.8 + - - +
408A GLU 3.6 13.7 - - - +
409A LEU 4.6 0.7 - - - +
410A THR* 1.3 79.2 - - - +
412A LEU* 1.3 61.2 + - - +
514A ARG* 2.7 38.9 + - - -
517A MET* 3.4 15.8 - - + +
428B PRO* 4.1 9.3 - - - +
430B PHE* 3.8 20.4 - - - -
383D ARG* 5.5 7.6 + - - +
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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