Contacts of the helix formed by residues 352 - 362 (chain B) in PDB entry 5DVX
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 SER 352 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281B GLU* 4.4 0.7 - - - -
282B GLY 3.6 10.3 - - - -
283B PRO 5.0 3.4 - - - -
284B GLU 3.5 17.4 + - - -
285B GLU* 4.0 13.3 + - - +
351B LEU* 1.3 75.5 - - - +
353B ALA* 1.3 65.0 + - - +
354B LYS* 3.4 9.6 + - - +
355B GLN* 3.0 38.5 + - - +
356B LEU* 3.0 21.3 + - - +
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Residues in contact with ALA 353 (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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281B GLU* 3.7 31.6 + - - +
282B GLY 4.3 1.4 + - - -
351B LEU 3.9 0.6 + - - -
352B SER* 1.3 72.1 - - - +
354B LYS* 1.3 63.8 + - - +
356B LEU* 3.3 7.2 + - - +
357B HIS* 3.0 23.6 + - - +
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Residues in contact with LYS 354 (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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285B GLU* 4.7 15.3 + - - +
290B GLU* 6.2 0.4 - - - -
352B SER* 3.4 7.9 + - - +
353B ALA* 1.3 79.3 - - - +
355B GLN* 1.3 58.9 + - + +
357B HIS* 3.2 8.8 + - + +
358B THR* 2.9 39.1 + - - +
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Residues in contact with GLN 355 (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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285B GLU* 3.4 12.9 - - + +
286B ASN* 2.8 55.0 + - - +
289B TYR* 4.4 0.4 - - - +
290B GLU* 3.1 31.6 + - - +
293B LEU* 3.5 23.3 - - + +
351B LEU* 3.6 9.4 - - + -
352B SER* 3.0 32.9 + - - +
354B LYS* 1.3 79.7 - - + +
356B LEU* 1.3 56.5 + - - +
358B THR* 3.2 6.9 + - - -
359B LEU* 3.0 28.4 + - - +
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Residues in contact with LEU 356 (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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247B PRO* 4.2 24.5 - - + -
248B ALA* 4.5 17.0 - - + -
279B LEU* 4.7 6.1 - - + -
280B GLU 4.1 2.9 - - - -
281B GLU* 3.8 41.5 - - + +
351B LEU* 3.9 24.9 - - + +
352B SER 3.0 14.9 + - - +
353B ALA* 3.7 7.6 - - - +
355B GLN* 1.3 75.3 - - - +
357B HIS* 1.3 61.2 + - - +
359B LEU* 3.4 9.9 + - + +
360B SER* 3.2 24.9 + - - -
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Residues in contact with HIS 357 (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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232B ALA* 4.9 19.4 - - + +
353B ALA 3.0 12.8 + - - +
354B LYS* 3.5 11.7 + - - +
356B LEU* 1.3 74.3 - - - +
358B THR* 1.3 63.9 + - - +
360B SER* 3.2 6.9 + - - -
361B ASP* 2.8 71.1 + - + +
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Residues in contact with THR 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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293B LEU* 3.8 34.1 - - + +
296B LEU* 3.9 5.6 - - + +
354B LYS* 2.9 25.7 + - - +
355B GLN* 3.2 11.9 + - - -
357B HIS* 1.3 81.2 + - - +
359B LEU* 1.3 62.2 + - - +
361B ASP* 5.0 0.7 - - - -
362B THR* 2.6 39.9 + - + +
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Residues in contact with LEU 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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202B VAL* 4.7 2.2 - - + -
227B LEU* 3.7 32.8 - - + -
229B TRP* 3.6 55.7 - - + -
248B ALA* 4.2 16.6 - - + -
279B LEU* 4.6 9.6 - - + -
293B LEU* 4.0 17.2 - - + +
296B LEU* 4.0 17.3 - - + +
351B LEU* 5.0 2.7 - - + -
355B GLN 3.0 13.5 + - - +
356B LEU* 3.6 16.2 - - + +
357B HIS 3.2 0.2 - - - -
358B THR* 1.3 79.5 - - - +
360B SER* 1.3 59.2 + - - +
362B THR 4.4 2.1 + - - -
363B LEU* 4.9 4.2 + - - +
371B LEU 5.0 0.2 - - - +
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Residues in contact with SER 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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229B TRP* 3.5 27.6 - - - -
230B GLY 3.8 15.9 - - - -
231B ALA* 4.3 2.4 - - - -
232B ALA* 4.1 14.6 + - - -
356B LEU 3.2 15.2 + - - -
357B HIS* 3.4 8.3 + - - -
359B LEU* 1.3 78.8 - - - +
361B ASP* 1.3 61.4 + - - +
362B THR 3.6 0.7 - - - -
363B LEU 5.2 1.4 + - - +
370B ARG* 5.1 0.2 + - - -
371B LEU 3.9 3.4 - - - +
372B GLN* 3.0 31.4 + - - +
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Residues in contact with ASP 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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232B ALA* 6.5 0.2 - - + -
357B HIS* 2.8 52.0 + - + +
358B THR* 4.8 0.7 - - - +
360B SER* 1.3 79.4 - - - +
362B THR* 1.3 64.3 + - - +
363B LEU 3.8 1.6 - - - -
370B ARG* 3.1 43.0 + - - +
372B GLN* 4.4 2.2 - - - +
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Residues in contact with THR 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B LEU* 3.7 19.5 - - + +
297B GLU* 3.6 46.1 - - + +
300B ALA* 3.5 15.6 - - + +
358B THR* 2.6 37.1 + - + +
359B LEU 4.4 0.2 + - - -
360B SER 3.6 0.2 - - - -
361B ASP* 1.3 81.7 + - - +
363B LEU* 1.3 63.0 + - + +
364B TRP* 4.7 4.3 + - - -
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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