Contacts of the helix formed by residues 358 - 367 (chain D) in PDB entry 5ZRV
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 ALA 358 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341D MET* 5.7 5.8 - - - -
343D VAL* 6.1 5.8 - - - +
354D GLY 4.1 4.2 + - - -
355D PRO* 2.8 10.8 + - - -
357D TYR* 1.3 79.3 - - - +
359D THR* 1.3 62.1 + - - +
360D PRO 3.5 1.1 - - - -
361D LYS* 3.2 13.9 + - - +
362D VAL* 3.3 9.0 + - - -
464D GLY* 6.5 0.7 - - - -
465D HIS 6.5 1.3 - - - -
466D ALA* 6.0 5.1 - - - +
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Residues in contact with THR 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355D PRO 3.1 11.5 + - - -
356D THR* 4.6 2.7 - - - +
357D TYR 3.8 1.0 - - - +
358D ALA* 1.3 76.0 - - - +
360D PRO* 1.3 57.6 - - - +
362D VAL* 3.0 16.6 + - - +
363D LEU* 3.0 11.8 + - - -
466D ALA* 6.2 3.1 - - - +
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Residues in contact with PRO 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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356D THR 5.9 0.8 - - - -
357D TYR 5.1 1.6 - - - -
358D ALA 3.5 0.6 - - - -
359D THR* 1.3 73.7 - - - +
361D LYS* 1.3 57.5 + - - -
362D VAL 3.4 0.2 - - - -
363D LEU* 4.1 4.7 - - - +
364D GLU* 3.8 13.7 + - - +
409D VAL* 5.5 8.8 - - - +
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Residues in contact with LYS 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D MET* 5.7 4.1 - - - -
357D TYR 5.0 2.8 + - - -
358D ALA* 3.2 10.2 + - - +
359D THR 3.1 1.4 - - - -
360D PRO* 1.3 78.9 - - - +
362D VAL* 1.3 57.5 + - - +
364D GLU* 4.7 0.4 - - - +
365D LYS* 3.7 14.4 + - - -
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Residues in contact with VAL 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D MET* 5.2 13.7 - - - +
358D ALA 3.3 6.7 + - - -
359D THR* 3.0 7.0 + - - +
361D LYS* 1.3 77.9 - - - +
363D LEU* 1.3 59.2 + - - +
364D GLU 3.4 0.2 - - - -
365D LYS* 3.6 3.3 - - - +
366D ALA* 2.9 24.6 + - - -
466D ALA 6.0 0.7 - - - -
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Residues in contact with LEU 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359D THR 3.0 13.4 + - - -
360D PRO* 4.1 3.1 - - - -
361D LYS 3.6 0.2 - - - -
362D VAL* 1.3 77.0 - - - +
364D GLU* 1.3 56.6 + - - +
366D ALA* 3.3 1.8 + - - +
367D GLY 2.8 23.4 + - - -
368D LEU 3.3 21.0 + - - -
369D THR 6.3 1.1 - - - -
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Residues in contact with GLU 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360D PRO 3.8 14.2 + - - -
361D LYS 5.0 0.4 - - - -
363D LEU* 1.3 72.9 - - - +
365D LYS* 1.3 64.8 + - - +
367D GLY* 3.5 10.6 + - - +
368D LEU 5.2 1.1 - - - -
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Residues in contact with LYS 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361D LYS 3.7 12.8 + - - -
362D VAL* 3.2 9.5 + - - +
363D LEU 3.2 0.8 - - - -
364D GLU* 1.3 79.7 - - - +
366D ALA* 1.3 59.0 + - - +
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Residues in contact with ALA 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D ASP* 6.4 1.6 - - - +
362D VAL 2.9 14.0 + - - -
363D LEU* 3.7 2.0 - - - +
365D LYS* 1.3 76.5 - - - +
367D GLY* 1.3 63.2 + - - +
368D LEU 3.9 0.2 - - - -
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Residues in contact with GLY 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363D LEU 2.8 10.3 + - - -
364D GLU* 3.5 9.3 + - - -
365D LYS 3.4 3.0 - - - -
366D ALA* 1.3 80.7 - - - +
368D LEU* 1.3 54.9 - - - -
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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