Contacts of the helix formed by residues 475 - 488 (chain C) in PDB entry 2VM8
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 PRO 475 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162C ASN* 4.4 4.3 - - - +
192C GLY 4.1 3.8 - - - +
194C ILE* 4.3 9.4 - - + -
390C LYS 3.7 17.9 - - - +
391C VAL 3.4 20.0 - - - +
393C ASN* 3.5 35.2 - - + +
472C LYS 4.1 3.6 - - - +
473C PRO* 3.4 4.8 - - + -
474C PHE* 1.3 88.6 - - - +
476C ASP* 1.3 60.6 + - - +
477C PHE 4.6 0.2 - - - +
478C VAL* 3.3 10.7 + - + -
479C TYR* 2.9 31.9 + - + +
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Residues in contact with ASP 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393C ASN* 5.0 1.8 + - - -
474C PHE 3.3 5.4 + - - +
475C PRO* 1.3 71.9 - - - +
477C PHE* 1.3 62.9 + - - +
479C TYR* 5.0 0.4 - - - -
480C LYS* 3.2 70.5 + - + +
483C LYS* 4.7 8.4 + - - +
29D GLN* 6.2 0.2 - - - +
30D SER* 5.1 10.4 + - - +
376D ASP* 3.9 3.1 - - - +
378D ASN* 5.1 1.6 - - - +
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Residues in contact with PHE 477 (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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275C TYR* 3.5 29.3 + + - -
327C GLN* 6.3 2.2 - - + -
387C ASN* 4.2 15.7 - - + -
390C LYS* 3.4 59.9 - - + +
391C VAL* 3.8 20.4 - - + -
475C PRO 3.3 0.4 - - - -
476C ASP* 1.3 77.7 - - - +
478C VAL* 1.3 58.3 + - - +
481C ARG* 2.9 26.3 + - - -
28D ASP 5.4 4.9 - - - -
376D ASP* 4.1 9.2 - - - +
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Residues in contact with VAL 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194C ILE* 4.9 6.5 - - + -
249C PRO* 3.0 43.5 - - + -
273C VAL* 3.7 9.1 - - + +
275C TYR* 3.1 31.2 - - + +
391C VAL* 4.1 28.7 - - + +
475C PRO* 3.3 10.6 + - + +
476C ASP 3.1 0.2 - - - -
477C PHE* 1.3 80.5 - - + +
479C TYR* 1.3 67.6 + - + +
480C LYS 3.7 1.5 + - - -
481C ARG* 4.0 8.0 + - - +
482C ILE* 3.1 19.7 + - + +
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Residues in contact with TYR 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188C ILE 3.4 8.1 + - - -
189C ARG* 3.6 19.2 - - + -
192C GLY* 3.4 19.5 - - - -
193C ALA 2.5 35.0 + - - -
194C ILE* 5.4 0.7 - - + -
249C PRO* 3.3 27.3 - - + +
474C PHE* 3.6 30.7 - + - +
475C PRO* 2.9 21.4 + - + +
476C ASP* 5.0 0.2 - - - -
478C VAL* 1.3 86.4 - - + +
480C LYS* 1.3 60.2 + - - +
481C ARG 3.2 1.8 - - - -
482C ILE* 3.5 29.4 - - + -
483C LYS* 2.9 49.1 + - + +
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Residues in contact with LYS 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476C ASP* 3.2 51.6 + - + +
479C TYR* 1.3 73.0 - - - +
481C ARG* 1.3 71.0 + - - +
483C LYS* 3.9 11.0 - - + +
484C ALA* 3.2 21.3 + - - +
487C ARG* 5.1 0.5 + - - -
23D LYS* 5.4 1.6 - - - +
30D SER* 3.4 14.1 + - - +
376D ASP* 3.3 23.3 - - + -
377D GLU* 2.6 35.9 + - + +
378D ASN* 2.8 29.7 + - - +
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Residues in contact with ARG 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C GLY 6.0 0.2 - - - -
272C THR 4.4 4.8 + - - -
273C VAL* 3.7 38.1 - - + +
274C VAL 5.1 0.8 - - - +
275C TYR* 2.9 23.0 + - - -
477C PHE* 2.9 32.1 + - - -
478C VAL 4.0 5.6 + - - +
480C LYS* 1.3 85.4 - - - +
482C ILE* 1.3 61.9 + - - +
484C ALA* 3.1 5.3 + - - +
485C ARG* 3.0 34.8 + - - +
373D GLY* 3.9 13.1 - - - +
374D LYS 3.5 24.5 - - - +
375D MET* 4.0 19.3 - - - +
376D ASP* 4.2 10.1 + - - +
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Residues in contact with ILE 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C ARG* 4.4 5.4 - - + -
247C ASN* 3.1 45.1 + - - +
249C PRO* 3.2 40.8 - - + -
273C VAL* 3.7 18.4 - - + -
478C VAL* 3.1 24.2 - - + +
479C TYR* 3.5 32.2 + - + +
480C LYS 3.4 0.6 - - - -
481C ARG* 1.3 74.2 - - - +
483C LYS* 1.3 67.4 + - + +
485C ARG* 3.3 3.1 + - - +
486C SER* 3.0 26.3 + - - +
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Residues in contact with LYS 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474C PHE* 3.9 44.8 + - + +
476C ASP* 4.7 9.3 + - - +
479C TYR* 2.9 37.0 + - + +
480C LYS* 3.9 9.6 - - + +
482C ILE* 1.3 72.5 - - + +
484C ALA* 1.3 59.7 + - - +
486C SER* 2.7 30.5 + - - -
487C ARG* 3.3 31.9 + - - +
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Residues in contact with ALA 484 (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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480C LYS 3.2 9.0 + - - +
481C ARG* 3.1 10.0 + - - +
483C LYS* 1.3 79.0 - - - +
485C ARG* 1.3 61.0 + - - +
487C ARG* 3.2 36.4 + - - +
488C LEU* 3.5 15.9 - - - +
370D VAL 4.3 17.5 - - - +
371D VAL* 5.2 4.0 - - - +
373D GLY* 4.3 8.3 - - - +
375D MET 6.1 0.2 - - - +
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Residues in contact with ARG 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244C ASN* 5.0 5.1 + - - -
247C ASN* 3.8 25.9 + - - +
271C GLY* 2.8 34.3 + - - -
272C THR* 4.7 0.8 - - - +
273C VAL* 3.8 24.9 - - - +
481C ARG* 3.0 28.0 + - - +
482C ILE* 3.7 6.5 - - - +
483C LYS 3.2 0.2 - - - -
484C ALA* 1.3 77.2 - - - +
486C SER* 1.3 58.8 + - - +
487C ARG 3.3 0.6 + - - -
488C LEU* 3.8 27.3 + - + +
489C ALA 5.6 0.2 - - - +
372D THR 4.6 1.1 - - - +
373D GLY* 2.7 36.8 + - - +
374D LYS* 4.1 8.1 + - - +
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Residues in contact with SER 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189C ARG* 4.9 6.6 - - - -
247C ASN* 3.2 12.3 + - - +
482C ILE* 3.0 16.5 + - - +
483C LYS* 2.7 21.5 + - - -
485C ARG* 1.3 71.5 - - - +
487C ARG* 1.3 61.1 + - - +
488C LEU 3.3 4.7 - - - +
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Residues in contact with ARG 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C LYS 5.1 0.4 + - - -
483C LYS* 3.3 35.0 + - - +
484C ALA* 3.2 39.6 + - - +
486C SER* 1.3 76.2 - - - +
488C LEU* 1.3 67.9 + - + +
440D ARG* 6.2 2.0 - - - +
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Residues in contact with LEU 488 (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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484C ALA 3.5 11.4 - - - +
485C ARG* 3.8 27.7 + - + +
486C SER 3.3 6.6 - - - +
487C ARG* 1.3 83.2 - - + +
489C ALA* 1.3 69.1 + - - +
371D VAL* 3.5 24.0 - - + +
372D THR* 3.5 26.2 - - - +
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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