Contacts of the helix formed by residues 308 - 316 (chain J) in PDB entry 1MVW
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 ASN 308 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292J MET* 3.4 1.8 - - - -
306J THR* 3.5 4.4 + - - +
307J THR* 1.3 75.3 + - - +
309J PRO* 1.3 64.8 - - - +
310J TYR* 2.8 39.5 + - - +
311J ASP* 3.1 41.6 + - - +
312J TYR* 3.7 1.7 - - - -
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Residues in contact with PRO 309 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289J TYR* 4.7 11.0 - - + -
292J MET* 3.0 30.5 - - + -
307J THR 3.1 7.2 - - - +
308J ASN* 1.3 84.5 - - - +
310J TYR* 1.3 58.0 + - + +
311J ASP 2.8 11.8 + - - -
312J TYR* 2.9 17.1 + - + +
315J VAL* 4.5 3.1 - - + +
316J SER* 3.3 17.5 - - - -
320J ILE* 3.5 45.1 - - + -
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Residues in contact with TYR 310 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308J ASN* 2.8 27.9 + - - +
309J PRO* 1.3 81.5 - - + +
311J ASP* 1.3 59.8 + - - +
312J TYR 3.3 2.9 - - - -
313J HIS* 5.0 1.8 + - - -
316J SER* 3.8 28.2 + - - -
318J GLY 5.3 5.4 + - - -
320J ILE* 2.8 35.7 - - + +
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Residues in contact with ASP 311 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306J THR* 2.5 30.0 + - - +
308J ASN* 3.1 19.3 + - - +
309J PRO 2.8 0.4 + - - -
310J TYR* 1.3 79.8 - - - +
312J TYR* 1.3 77.9 + - + +
313J HIS 3.8 1.6 - - - -
363J ASN* 2.6 35.5 + - - +
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Residues in contact with TYR 312 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292J MET* 4.4 11.9 - - + -
304J LEU 4.3 0.7 + - - -
305J ILE* 2.9 31.4 - - + -
306J THR* 2.7 36.6 + - - +
308J ASN 3.7 7.2 - - - -
309J PRO* 2.9 17.9 + - + +
311J ASP* 1.3 107.3 - - + +
313J HIS* 1.3 54.7 - - - +
314J TYR* 3.2 3.1 - - + +
315J VAL* 2.8 39.7 + - + +
316J SER* 3.4 3.5 + - - -
359J MET* 3.6 34.8 - - + +
360J HIS* 4.2 12.5 + + - -
363J ASN* 3.8 15.9 - - - -
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Residues in contact with HIS 313 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276J THR 5.6 0.2 + - - -
310J TYR 5.0 1.8 + - - -
311J ASP 3.8 1.8 - - - -
312J TYR* 1.3 72.6 - - - +
314J TYR* 1.3 80.8 + + - +
315J VAL 3.0 1.0 + - - -
316J SER* 3.4 12.6 + - - -
317J GLU* 3.2 46.2 + - + +
362J GLY 4.1 19.1 - - - +
363J ASN* 4.0 6.0 + - - +
365J LYS* 5.4 7.0 - - - +
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Residues in contact with TYR 314 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274J ARG 4.1 0.3 - - - +
275J VAL 3.7 21.1 - - - +
276J THR* 3.8 36.2 - - + +
278J GLN* 3.1 20.7 + - - +
312J TYR 3.1 2.2 + - - +
313J HIS* 1.3 91.7 - + - +
315J VAL* 1.3 65.9 + - + +
317J GLU* 4.4 0.2 - - - -
358J VAL* 3.4 24.0 - - + +
359J MET* 4.5 5.8 - - - +
361J TYR 4.1 0.9 - - - -
362J GLY* 3.1 39.3 - - - -
423J HIS 4.6 2.8 + - - -
426J VAL* 3.8 8.1 - - - +
427J GLY* 3.3 29.6 + - - -
430J ALA* 3.8 21.3 - - + -
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Residues in contact with VAL 315 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275J VAL 4.7 3.6 - - - +
278J GLN* 2.8 9.6 - - - +
284J SER* 4.6 4.5 - - - -
288J PHE* 4.0 42.4 - - + -
289J TYR* 2.3 51.0 + - + +
292J MET* 4.8 3.8 - - - -
309J PRO* 4.5 9.4 - - + +
312J TYR* 2.8 27.9 + - + +
314J TYR* 1.3 88.7 - - + +
316J SER* 1.3 55.2 + - - -
319J GLU 4.4 0.2 - - - +
359J MET* 4.7 10.5 - - + -
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Residues in contact with SER 316 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278J GLN* 2.8 0.4 + - - -
309J PRO* 3.3 34.4 + - - -
310J TYR* 3.8 32.9 + - - -
312J TYR 3.4 4.4 + - - -
313J HIS* 3.4 9.1 + - - -
315J VAL* 1.3 80.5 - - - +
317J GLU* 1.3 62.7 + - - +
318J GLY 3.2 7.2 - - - +
319J GLU 5.0 1.8 - - - -
320J ILE* 4.5 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