Contacts of the helix formed by residues 391 - 403 (chain A) in PDB entry 6QVC
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 LEU 391 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A LEU* 5.6 16.4 - - + +
176A ALA* 6.4 1.8 - - + -
177A LEU* 5.7 11.9 - - + -
180A HIS* 6.0 6.5 - - + -
389A HIS* 3.4 23.1 - - + +
390A ARG* 1.3 81.5 - - + +
392A LEU* 1.3 61.6 + - - +
393A TYR 3.4 0.6 + - - -
394A PRO* 3.7 11.0 - - - +
395A GLY* 4.7 3.5 + - - -
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Residues in contact with LEU 392 (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 PHE* 4.0 27.6 - - + -
389A HIS* 3.8 33.6 + - + +
390A ARG 3.2 1.6 - - - -
391A LEU* 1.3 80.8 - - - +
393A TYR* 1.3 67.2 + - - +
394A PRO 3.6 0.3 - - - -
395A GLY 4.0 0.5 + - - -
396A ILE* 3.2 54.7 + - + +
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Residues in contact with TYR 393 (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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372A VAL* 5.5 1.6 - - - +
376A VAL* 5.3 4.1 - - + +
382A LEU* 5.9 8.7 - - + -
386A LEU* 4.0 24.9 - - + +
389A HIS 5.0 0.6 + - - -
390A ARG 3.7 2.0 + - - +
391A LEU 3.4 0.2 - - - -
392A LEU* 1.3 84.1 - - - +
394A PRO* 1.4 70.8 - - + +
396A ILE* 3.6 14.9 - - + +
397A VAL* 4.0 22.6 - - + +
473A VAL* 5.1 5.0 + - - +
476A THR* 3.3 28.0 - - + +
477A MET* 3.8 25.7 + - + -
478A PRO* 3.8 17.9 - - + -
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Residues in contact with PRO 394 (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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172A ILE* 4.6 9.9 - - + -
176A ALA* 4.7 17.9 - - + -
390A ARG 4.0 7.6 - - - +
391A LEU* 3.7 11.4 - - - +
393A TYR* 1.4 94.6 - - + +
395A GLY* 1.3 67.0 + - - +
397A VAL* 3.0 19.5 + - + +
398A THR* 3.1 14.8 + - - -
477A MET* 4.0 24.6 - - + +
478A PRO* 4.0 28.9 - - + +
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Residues in contact with GLY 395 (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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169A LEU* 4.5 19.8 - - - +
172A ILE* 4.9 6.7 - - - +
173A LEU* 5.9 3.8 - - - -
391A LEU 4.7 2.9 + - - -
392A LEU 4.0 2.6 + - - -
393A TYR 3.6 0.4 - - - -
394A PRO* 1.3 81.5 - - - +
396A ILE* 1.3 52.7 + - - +
398A THR* 2.9 13.3 - - - -
399A PHE* 2.7 33.2 + - - +
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Residues in contact with ILE 396 (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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169A LEU* 6.0 1.8 - - + -
392A LEU* 3.2 51.8 + - + +
393A TYR* 3.6 9.4 - - + +
395A GLY* 1.3 75.0 - - - +
397A VAL* 1.3 87.1 + - + +
399A PHE* 2.8 35.2 - - + +
400A VAL* 2.9 8.8 + - - +
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Residues in contact with VAL 397 (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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393A TYR* 4.0 23.8 - - + +
394A PRO* 3.0 19.0 + - + +
396A ILE* 1.3 93.5 - - + +
398A THR* 1.3 65.4 + - - +
400A VAL* 3.1 16.4 + - + +
401A ILE* 2.9 28.8 + - + +
473A VAL* 4.0 27.4 - - + -
477A MET* 4.2 12.8 - - + -
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Residues in contact with THR 398 (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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168A PRO* 4.4 7.6 - - + +
169A LEU* 4.4 15.9 - - + +
172A ILE* 3.9 24.4 - - + +
227A ILE* 3.9 27.7 - - + +
394A PRO 3.1 16.3 + - - -
395A GLY* 2.9 16.1 + - - +
397A VAL* 1.3 76.1 - - - +
399A PHE* 1.3 53.1 + - - +
401A ILE* 3.1 14.2 + - - +
402A ALA* 2.9 29.6 + - + +
477A MET* 4.2 12.1 - - - +
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Residues in contact with PHE 399 (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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161A PHE* 5.3 11.0 - + - -
165A VAL* 4.1 31.7 - - + +
169A LEU* 5.0 17.9 - - + +
395A GLY 2.7 12.6 + - - +
396A ILE* 2.8 25.6 - - + +
398A THR* 1.3 71.7 - - - +
400A VAL* 1.3 67.9 + - + -
402A ALA* 3.1 10.5 + - - +
403A SER* 2.9 29.8 + - - -
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Residues in contact with VAL 400 (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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396A ILE 2.9 12.3 + - - +
397A VAL* 3.1 28.0 + - + +
399A PHE* 1.3 83.6 - - + +
401A ILE* 1.3 66.8 + - + +
403A SER* 3.0 32.6 + - - +
404A PHE* 3.4 22.4 + - + -
469A TRP* 6.4 2.2 - - + -
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Residues in contact with ILE 401 (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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227A ILE* 3.6 34.5 - - + -
228A PRO* 5.0 5.6 - - + -
397A VAL 2.9 16.2 + - - +
398A THR* 3.3 16.6 - - - +
400A VAL* 1.3 82.8 - - + +
402A ALA* 1.3 54.7 - - - +
404A PHE* 3.0 18.4 + - + +
405A THR* 2.2 27.1 + - - +
466A MET* 5.6 0.4 - - + -
469A TRP* 5.1 11.9 - - + -
470A MET* 3.7 49.0 - - + +
473A VAL* 5.3 12.6 - - + -
474A ALA* 5.4 3.8 - - + +
477A MET* 6.1 2.9 - - + -
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Residues in contact with ALA 402 (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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161A PHE* 5.4 0.4 - - - -
164A TRP* 3.3 39.2 + - + +
165A VAL* 4.8 11.4 - - + +
168A PRO* 5.6 6.7 - - + -
227A ILE* 5.9 3.8 - - + -
398A THR* 2.9 15.2 + - + +
399A PHE* 3.1 12.5 + - - +
401A ILE* 1.3 78.4 - - - +
403A SER* 1.3 56.5 + - - +
405A THR* 3.0 24.8 + - - -
406A PHE* 3.4 4.0 + - - +
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Residues in contact with SER 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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161A PHE* 4.9 19.9 - - - -
165A VAL* 5.6 0.8 - - - +
399A PHE* 2.9 17.9 + - - -
400A VAL* 3.0 27.0 + - - +
402A ALA* 1.3 76.9 - - - +
404A PHE* 1.3 71.6 + - - +
406A PHE* 4.9 4.8 + - - +
410A MET* 4.7 4.5 - - - +
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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