Contacts of the helix formed by residues 308 - 316 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D MET* 3.4 1.8 - - - -
306D THR* 3.6 3.7 + - - +
307D THR* 1.3 75.9 + - - +
309D PRO* 1.3 64.7 - - - +
310D TYR* 2.8 38.6 + - - +
311D ASP* 3.1 42.4 + - - +
312D TYR* 3.7 1.4 - - - -
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Residues in contact with PRO 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D TYR* 4.7 11.9 - - + -
292D MET* 3.0 29.4 - - + -
307D THR 3.1 7.4 - - - +
308D ASN* 1.3 85.1 - - - +
310D TYR* 1.3 59.5 + - + +
311D ASP 2.8 11.4 + - - -
312D TYR* 2.9 18.1 + - + +
315D VAL* 4.8 2.9 - - + -
316D SER* 3.3 17.4 - - - -
320D ILE* 3.5 45.5 - - + -
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Residues in contact with TYR 310 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D ASN* 2.8 30.5 + - - +
309D PRO* 1.3 79.2 - - + +
311D ASP* 1.3 58.5 + - - +
312D TYR 3.3 2.9 - - - -
313D HIS 5.0 1.4 + - - -
316D SER* 3.8 28.7 - - - -
318D GLY 5.6 2.5 - - - -
320D ILE* 2.8 36.4 - - + +
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Residues in contact with ASP 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306D THR* 2.5 30.1 + - - +
308D ASN* 3.1 18.9 + - - +
309D PRO 2.8 0.4 + - - -
310D TYR* 1.3 79.4 - - - +
312D TYR* 1.3 76.2 - - + +
313D HIS 3.8 1.8 - - - -
363D ASN* 2.6 35.8 + - - +
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Residues in contact with TYR 312 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292D MET* 4.4 12.3 - - + -
304D LEU 4.3 0.5 + - - -
305D ILE* 2.9 29.9 - - + -
306D THR* 2.7 37.6 + - - +
308D ASN 3.7 7.0 - - - -
309D PRO* 2.9 18.0 + - + +
310D TYR 4.8 0.2 - - - -
311D ASP* 1.3 107.0 + - + +
313D HIS* 1.3 55.5 + - - +
314D TYR* 3.2 2.9 - - + +
315D VAL* 2.8 38.0 + - + +
316D SER* 3.4 5.2 + - - -
359D MET* 3.6 35.2 - - + +
360D HIS* 4.2 12.9 + + - -
363D ASN* 3.8 16.2 - - - -
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Residues in contact with HIS 313 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276D THR 5.6 0.4 + - - -
310D TYR 5.0 2.0 + - - -
311D ASP 3.8 2.0 - - - -
312D TYR* 1.3 71.5 - - - +
314D TYR* 1.3 82.0 + + - +
315D VAL 3.0 1.0 + - - -
316D SER* 3.4 11.5 + - - -
317D GLU* 3.2 44.9 + - + +
362D GLY 4.1 18.4 - - - +
363D ASN* 4.0 5.8 + - - +
365D LYS* 5.4 7.0 - - - +
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Residues in contact with TYR 314 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274D ARG 4.1 0.2 - - - +
275D VAL 3.7 21.8 - - - +
276D THR* 3.8 36.6 - - + -
278D GLN* 3.1 20.3 + - - +
312D TYR 3.2 2.2 - - - +
313D HIS* 1.3 93.4 - + - +
315D VAL* 1.3 67.0 + - + +
317D GLU* 3.9 0.4 - - - +
358D VAL* 3.4 24.2 - - + +
359D MET* 4.5 5.8 - - - +
361D TYR 4.1 0.8 + - - -
362D GLY* 3.1 40.0 + - - -
423D HIS 4.6 3.1 + - - -
426D VAL* 3.8 8.1 - - - +
427D GLY* 3.3 29.5 + - - -
430D ALA* 3.8 20.2 - - + -
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Residues in contact with VAL 315 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D VAL 4.7 3.8 - - - +
278D GLN* 2.8 9.9 - - - +
284D SER* 4.6 4.3 - - - -
288D PHE* 4.0 43.5 - - + -
289D TYR* 2.3 48.8 + - + +
292D MET* 4.8 3.8 - - - -
309D PRO* 4.5 9.6 - - + +
312D TYR* 2.8 26.8 + - + +
314D TYR* 1.3 89.6 - - + +
316D SER* 1.3 55.1 + - - -
319D GLU 4.4 0.2 - - - +
359D MET* 4.7 11.0 - - + -
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Residues in contact with SER 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278D GLN* 3.4 0.2 - - - -
309D PRO* 3.3 34.5 + - - -
310D TYR* 3.8 32.0 - - - -
312D TYR 3.4 5.4 + - - -
313D HIS* 3.4 9.9 + - - -
315D VAL* 1.3 80.7 - - - +
317D GLU* 1.3 63.9 + - - +
318D GLY 3.2 6.6 - - - +
319D GLU 5.0 1.6 - - - -
320D 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