Contacts of the helix formed by residues 357 - 367 (chain B) in PDB entry 3M0V
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 ASP 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B ARG 5.5 2.9 - - - +
355B LEU 3.3 4.1 + - - +
356B VAL* 1.3 71.8 - - - +
358B ARG* 1.3 57.7 + - - +
359B ALA* 3.2 11.8 + - - +
360B ALA* 2.9 33.9 + - + +
361B LEU* 2.9 27.5 + - - +
376B THR* 3.8 11.4 + - + +
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Residues in contact with ARG 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B ASN* 2.9 34.9 + - - +
310B VAL* 3.3 31.0 - - + +
311B ASP* 3.6 34.6 + - - +
314B ALA* 4.6 17.5 - - + -
353B ALA 3.1 24.7 + - - -
356B VAL* 3.0 23.8 + - - +
357B ASP* 1.3 71.4 + - - +
359B ALA* 1.3 57.3 + - - +
361B LEU* 3.7 14.9 - - - +
362B SER* 2.9 30.8 + - - -
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Residues in contact with ALA 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B ASP* 3.2 8.8 + - - +
358B ARG* 1.3 75.8 - - - +
360B ALA* 1.3 66.4 + - - +
362B SER* 3.3 7.3 + - - -
363B GLY* 3.1 17.8 + - - -
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Residues in contact with ALA 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357B ASP* 2.9 31.3 + - + +
359B ALA* 1.3 76.0 - - - +
361B LEU* 1.3 64.7 + - - +
363B GLY* 3.1 3.9 + - - -
364B TYR* 3.0 44.3 + - + +
376B THR* 4.5 4.5 - - + -
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307B ASN* 4.9 4.0 - - - +
356B VAL* 4.1 10.3 - - + -
357B ASP 2.9 16.8 + - - +
358B ARG* 3.7 18.6 - - - +
360B ALA* 1.3 77.7 - - - +
362B SER* 1.3 62.1 + - - +
364B TYR* 3.1 4.7 + - - -
365B GLN* 2.9 45.2 + - - +
373B ALA* 3.4 31.2 - - - +
376B THR* 4.0 11.6 - - + +
377B LEU* 4.0 22.7 - - + -
188D GLY* 3.5 22.7 - - - +
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Residues in contact with SER 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358B ARG 2.9 19.4 + - - -
359B ALA* 3.5 7.0 - - - -
361B LEU* 1.3 76.1 - - - +
363B GLY* 1.3 58.5 + - - +
365B GLN* 3.2 14.0 + - - +
366B GLU* 3.0 38.9 + - - +
194D ARG* 5.9 1.0 + - - -
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Residues in contact with GLY 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B ALA 3.1 7.2 + - - -
360B ALA* 3.1 8.4 + - - -
362B SER* 1.3 79.3 - - - +
364B TYR* 1.3 62.2 + - - +
366B GLU* 3.4 5.4 + - - +
367B ASP* 3.1 35.5 + - - +
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Residues in contact with TYR 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B ALA* 3.0 34.5 + - + +
361B LEU 3.1 5.6 + - - +
363B GLY* 1.3 74.5 - - - +
365B GLN* 1.3 63.7 + - - +
367B ASP* 3.7 2.9 + - + -
368B ASN* 3.2 1.7 + - - -
369B ASP* 2.8 60.4 + - + +
372B MET* 3.5 48.0 - - + +
373B ALA* 3.8 9.6 - - + -
376B THR* 3.3 26.7 - - - -
379B ARG* 5.7 0.3 + - - -
407C ARG* 5.1 1.8 - - - -
189D GLN 4.9 0.5 - - - +
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Residues in contact with GLN 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B LEU* 2.9 37.5 + - + +
362B SER* 3.5 15.6 - - - +
363B GLY 3.2 0.2 - - - -
364B TYR* 1.3 76.6 - - - +
366B GLU* 1.3 69.0 + - - +
368B ASN* 3.1 15.1 + - - -
373B ALA* 4.6 0.4 - - + -
149D THR* 3.6 15.7 - - + +
188D GLY* 2.9 31.0 + - - +
189D GLN 3.6 16.2 - - - +
190D SER* 3.7 16.6 + - - -
191D ASN* 3.6 29.3 + - + +
194D ARG* 5.5 2.3 - - - -
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Residues in contact with GLU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B SER* 3.0 28.3 + - - +
363B GLY* 3.9 6.1 - - - +
365B GLN* 1.3 80.1 - - - +
367B ASP* 1.3 63.8 + - - +
368B ASN* 3.3 0.7 - - - +
149D THR* 3.1 44.0 + - - +
194D ARG* 5.0 9.7 - - - -
198D ARG* 4.2 16.2 + - - -
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Residues in contact with ASP 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B GLY* 3.1 21.8 + - - +
364B TYR* 4.5 4.7 - - + +
366B GLU* 1.3 80.4 - - - +
368B ASN* 1.3 71.1 + - - +
369B ASP* 3.2 7.6 + - + +
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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