Contacts of the helix formed by residues 344 - 351 (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 GLY 344 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218C THR 4.8 0.5 - - - +
295C TRP* 3.6 2.2 + - - -
341C LYS 3.0 8.1 + - - -
343C VAL* 1.3 78.9 - - - +
345C LYS* 1.3 62.9 + - - +
346C ASP 3.2 3.1 - - - -
347C ASN 3.2 22.9 + - - +
348C PHE 4.0 0.3 + - - -
350C LEU* 3.8 4.4 + - - -
351C ILE* 3.1 43.6 - - - +
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Residues in contact with LYS 345 (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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218C THR* 4.7 4.2 - - - +
219C GLY* 5.6 0.5 - - - -
295C TRP* 3.3 36.9 + - + -
342C ALA* 2.8 38.2 + - + +
343C VAL 3.2 1.4 - - - +
344C GLY* 1.3 71.7 - - - +
346C ASP* 1.3 88.8 + - - +
347C ASN 3.9 0.2 + - - -
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Residues in contact with ASP 346 (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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218C THR* 3.7 23.4 - - - +
343C VAL 4.6 2.9 + - - +
344C GLY 3.2 0.4 - - - -
345C LYS* 1.3 115.6 + - - +
347C ASN* 1.3 60.7 + - + +
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Residues in contact with ASN 347 (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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213C LEU* 3.3 27.3 - - - +
218C THR* 4.0 3.0 + - - -
343C VAL 5.4 0.2 + - - -
344C GLY* 3.2 16.7 + - - +
345C LYS 3.6 0.8 + - - -
346C ASP* 1.3 82.6 - - + +
348C PHE* 1.3 65.3 + - - +
349C THR* 2.4 36.5 + - - +
350C LEU* 3.0 34.9 + - + +
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Residues in contact with PHE 348 (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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209C GLN* 3.8 20.6 - - + -
212C ILE* 4.1 6.1 - - + -
213C LEU* 3.6 25.8 - - + -
217C ILE 3.9 14.1 - - - -
218C THR 3.1 16.9 + - - +
219C GLY 3.6 15.9 - - - +
220C PRO* 4.3 4.7 - - + +
222C GLY* 3.4 35.0 - - - -
223C HIS* 3.5 29.1 + - + +
226C SER* 3.7 13.7 - - - -
302C VAL* 5.0 1.7 - - - +
347C ASN* 1.3 72.6 - - - +
349C THR* 1.3 78.7 + - + +
350C LEU 3.0 5.2 + - - -
351C ILE* 3.1 34.6 + - + +
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Residues in contact with THR 349 (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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81C GLN* 5.1 0.2 + - - -
209C GLN* 3.8 28.2 + - + +
213C LEU* 3.7 20.6 - - + +
223C HIS* 6.0 0.7 - - - -
347C ASN* 2.4 35.6 + - - +
348C PHE* 1.3 100.6 - - + +
350C LEU* 1.3 64.6 + - - +
351C ILE 3.6 0.7 - - - -
1491C MG 3.6 14.1 - - - -
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Residues in contact with LEU 350 (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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81C GLN* 3.1 32.9 + - - +
343C VAL* 3.5 31.7 - - + +
344C GLY* 3.8 7.4 - - - -
347C ASN* 3.0 31.2 + - + +
349C THR* 1.3 86.8 - - - +
351C ILE* 1.3 66.1 + - - +
352C PRO 3.3 1.0 - - - -
1491C MG 4.4 0.4 - - - -
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Residues in contact with ILE 351 (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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218C THR 5.5 0.2 - - - +
219C GLY 5.4 0.2 - - - -
220C PRO* 4.2 17.3 - - + -
295C TRP* 3.8 15.7 - - + +
299C ALA* 4.2 5.8 - - + -
302C VAL* 3.8 27.2 - - + +
341C LYS* 3.9 18.4 - - + +
344C GLY* 3.1 31.4 - - - +
348C PHE* 3.1 32.1 + - + +
349C THR 4.9 0.3 - - - +
350C LEU* 1.3 77.5 - - - +
352C PRO* 1.3 88.2 - - + +
353C GLU* 3.1 9.9 + - - +
1491C MG 3.8 7.4 - - - -
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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