Contacts of the helix formed by residues 381 - 394 (chain C) in PDB entry 2VF7
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 SER 381 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379C THR 4.4 0.2 + - - -
380C LEU* 1.3 76.2 - - - +
382C PRO* 1.3 74.2 - - - +
383C GLY* 3.5 4.6 + - - -
384C GLU* 3.1 36.4 + - - +
385C LEU* 3.2 20.0 + - - +
387C ARG* 5.3 0.2 + - - -
411C GLY* 5.8 3.1 - - - -
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Residues in contact with PRO 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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98C GLN* 4.1 20.3 + - - +
380C LEU 3.8 3.1 - - - +
381C SER* 1.3 86.0 - - - +
383C GLY* 1.3 61.2 + - - +
385C LEU* 3.6 8.8 + - + +
386C GLN* 3.1 26.1 + - - +
410C ALA* 5.5 6.1 - - + -
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Residues in contact with GLY 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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381C SER* 3.2 5.1 + - - -
382C PRO* 1.3 77.9 - - - +
384C GLU* 1.3 63.0 + - - +
386C GLN* 3.3 6.3 + - - +
387C ARG* 3.1 53.7 + - - +
407C GLU 5.3 2.0 - - - -
408C PRO 4.9 2.4 - - - +
410C ALA* 3.5 17.6 + - - +
411C GLY* 5.6 0.2 - - - -
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Residues in contact with GLU 384 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368C LEU* 3.8 12.5 - - + +
370C TYR* 2.7 41.1 + - + +
371C LEU* 4.4 4.9 - - + -
375C ARG* 4.0 8.4 + - - -
380C LEU* 3.4 28.6 - - + +
381C SER* 3.1 32.0 + - - +
383C GLY* 1.3 74.6 - - - +
385C LEU* 1.3 56.7 + - - +
387C ARG* 3.5 12.9 + - - +
388C LEU* 3.1 31.2 + - - +
532C SER* 5.0 3.4 + - - +
901C ADP 4.2 14.6 + - - -
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Residues in contact with LEU 385 (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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97C LEU 4.4 10.8 - - - +
98C GLN* 5.1 11.9 - - + -
99C GLN 6.0 0.7 - - - +
105C THR* 6.1 5.2 - - + -
113C VAL* 5.6 1.0 - - - +
377C THR* 4.2 33.7 - - + +
380C LEU* 4.4 16.2 - - + +
381C SER 3.2 12.3 + - - +
382C PRO* 4.2 11.9 - - + +
384C GLU* 1.3 74.1 - - - +
386C GLN* 1.3 68.9 + - + +
387C ARG 3.2 1.6 - - - -
388C LEU* 3.7 9.5 - - + +
389C ARG* 3.0 31.9 + - + +
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Residues in contact with GLN 386 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97C LEU* 4.3 16.6 - - + +
98C GLN* 3.1 28.6 - - - +
382C PRO 3.1 17.8 + - - +
383C GLY* 3.8 4.4 - - - +
385C LEU* 1.3 82.2 - - + +
387C ARG* 1.3 52.7 + - - +
389C ARG* 3.2 6.5 - - - +
390C LEU* 2.8 32.6 + - + +
405C LEU* 3.8 14.3 - - + +
406C ASP* 2.7 48.6 + - - -
407C GLU 3.7 10.9 + - - -
408C PRO* 4.0 17.9 - - + +
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Residues in contact with ARG 387 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
366C LEU* 4.3 26.4 - - + +
368C LEU* 3.7 22.1 - - + +
370C TYR* 5.4 0.2 + - - -
383C GLY* 3.1 34.2 + - - +
384C GLU* 3.5 18.7 - - - +
386C GLN* 1.3 74.3 - - + +
388C LEU* 1.3 58.8 + - - +
389C ARG 3.3 0.2 - - - -
390C LEU* 3.7 10.6 - - + +
391C ALA* 3.0 27.7 + - - +
408C PRO* 3.1 24.7 + - + +
409C SER 3.8 0.6 + - - -
410C ALA 2.1 35.6 + - - -
411C GLY 3.6 16.1 + - - -
412C LEU* 3.6 27.5 - - - +
420C LEU* 4.8 9.9 - - + -
532C SER* 4.7 7.7 + - - -
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Residues in contact with LEU 388 (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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110C VAL* 4.0 18.2 - - + -
113C VAL* 4.5 15.3 - - + -
114C THR* 3.7 17.4 - - + +
317C LEU* 4.7 2.0 - - + -
363C LEU* 3.5 25.6 - - + -
368C LEU* 4.1 10.5 - - + -
371C LEU* 3.7 28.3 - - + -
380C LEU* 3.8 24.2 - - + -
384C GLU 3.1 24.8 + - - +
385C LEU* 3.8 7.2 - - + +
386C GLN 3.4 0.4 - - - -
387C ARG* 1.3 74.6 - - - +
389C ARG* 1.3 60.6 + - - +
391C ALA* 3.6 2.4 + - - +
392C THR* 2.9 28.7 + - - -
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Residues in contact with ARG 389 (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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95C VAL* 4.9 6.9 - - - +
96C ALA 2.9 26.2 + - - -
97C LEU* 3.4 36.4 + - + +
98C GLN* 4.9 2.2 - - - +
99C GLN 5.8 0.4 - - - +
113C VAL* 4.8 13.2 - - - +
385C LEU* 3.0 23.7 + - - +
386C GLN 3.2 5.8 - - - +
388C LEU* 1.3 75.2 - - - +
390C LEU* 1.3 65.5 + - - +
392C THR* 3.3 8.2 + - - -
393C GLN* 3.2 49.1 + - - +
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Residues in contact with LEU 390 (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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97C LEU* 3.7 19.7 - - + +
366C LEU* 4.9 4.7 - - + -
386C GLN 2.8 19.5 + - - +
387C ARG* 3.7 11.7 - - - +
388C LEU 3.4 0.2 - - - -
389C ARG* 1.3 73.3 - - - +
391C ALA* 1.3 62.6 + - - +
393C GLN* 3.1 13.7 + - - +
394C LEU* 3.2 13.3 + - + +
405C LEU* 4.5 7.6 - - + -
408C PRO* 5.1 2.0 - - + -
420C LEU* 3.7 30.7 - - + -
423C ALA* 4.2 28.5 - - + +
424C LEU* 4.1 16.2 - - + -
427C LEU* 4.0 26.0 - - + -
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Residues in contact with ALA 391 (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 VAL* 4.0 7.6 - - + +
363C LEU* 3.6 37.2 - - + -
366C LEU* 4.0 22.1 - - + +
368C LEU* 4.7 0.2 - - + -
387C ARG 3.0 18.1 + - - +
388C LEU 3.9 0.7 - - - +
389C ARG 3.3 0.2 - - - -
390C LEU* 1.3 76.3 - - - +
392C THR* 1.3 60.3 + - - +
394C LEU* 3.1 15.0 + - - +
395C TYR* 3.2 19.4 - - - -
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Residues in contact with THR 392 (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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113C VAL* 3.5 17.4 + - - +
114C THR* 3.4 21.7 - - - +
115C THR* 4.2 15.3 - - - +
388C LEU 2.9 22.4 + - - -
389C ARG* 3.6 8.0 - - - -
390C LEU 3.3 0.4 - - - -
391C ALA* 1.3 75.0 - - - +
393C GLN* 1.3 69.9 + - - +
395C TYR* 3.3 34.9 + - + +
396C SER* 3.6 11.2 + - - -
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Residues in contact with GLN 393 (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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95C VAL* 5.3 3.9 - - - +
97C LEU* 3.6 20.6 - - + +
389C ARG* 3.2 33.3 + - - +
390C LEU* 3.1 11.2 + - - +
392C THR* 1.3 78.7 - - - +
394C LEU* 1.3 56.7 + - - +
395C TYR 3.0 9.4 + - - -
396C SER* 3.0 31.4 + - - -
397C ASN 4.5 2.1 + - - -
398C LEU* 3.7 11.6 + - - +
403C TYR* 2.8 40.9 + - + +
427C LEU* 3.9 16.4 - - + +
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Residues in contact with LEU 394 (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 VAL* 3.5 30.4 - - + +
366C LEU* 4.1 7.2 - - + -
390C LEU* 3.2 17.2 + - + +
391C ALA* 3.1 12.0 + - - +
393C GLN* 1.3 75.5 - - - +
395C TYR* 1.3 59.3 + - - +
397C ASN 5.6 0.2 - - - -
423C ALA* 3.6 34.8 - - + +
426C ASN* 3.7 16.6 - - + +
427C LEU* 3.5 39.0 - - + +
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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