Contacts of the helix formed by residues 345 - 355 (chain B) in PDB entry 5CP2
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 345 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339B SER* 3.9 9.7 + - - -
344B ALA* 1.3 75.2 - - - +
346B THR* 1.3 65.8 + - - -
349B ALA* 3.0 23.0 + - - +
3P G 2.8 36.2 + - - -
4P T 4.5 3.4 - - - -
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Residues in contact with THR 346 (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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335B LEU* 6.5 0.4 - - - -
339B SER* 4.1 14.6 - - - +
345B GLY* 1.3 72.3 - - - -
347B LYS* 1.3 66.7 + - - +
349B ALA* 3.3 2.9 + - - +
350B GLN* 2.9 50.5 + - - +
3P G 3.4 5.1 + - - -
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Residues in contact with LYS 347 (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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346B THR* 1.3 85.5 + - - +
348B THR* 1.3 63.1 + - - +
350B GLN* 3.5 21.4 + - + +
351B MET* 3.1 22.5 + - - +
2P A 3.6 54.0 + - - +
3P G 3.1 16.6 + - - +
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Residues in contact with THR 348 (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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344B ALA* 4.1 4.0 - - + -
345B GLY 4.0 7.5 + - - -
347B LYS* 1.3 73.2 - - - +
349B ALA* 1.3 61.8 + - - +
351B MET* 3.3 11.2 + - + +
352B TRP* 2.9 71.8 + - + +
373B GLN* 4.2 14.2 + - - +
2P A 4.1 3.3 + - - -
3P G 2.8 26.3 + - - -
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Residues in contact with ALA 349 (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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335B LEU* 3.6 18.1 - - + +
338B PHE* 3.7 32.2 - - + -
339B SER* 3.8 16.2 - - - +
344B ALA* 5.3 0.2 - - - +
345B GLY 3.0 18.2 + - - +
346B THR* 3.6 4.9 - - - +
348B THR* 1.3 77.9 - - - +
350B GLN* 1.3 56.3 + - - +
352B TRP* 3.3 6.0 + - - +
353B TYR* 2.9 28.1 + - - +
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Residues in contact with GLN 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335B LEU* 3.9 27.6 - - + +
346B THR* 2.9 36.9 + - - +
347B LYS* 3.8 22.9 + - - +
349B ALA* 1.3 77.4 - - - +
351B MET* 1.3 55.9 + - - +
353B TYR* 3.2 4.3 + - - +
354B GLN* 3.0 28.3 + - - +
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Residues in contact with MET 351 (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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347B LYS 3.1 17.0 + - - +
348B THR* 3.7 9.9 - - + +
350B GLN* 1.3 76.6 - - - +
352B TRP* 1.3 79.2 + - + +
354B GLN* 3.2 10.5 + - + +
355B GLN* 3.0 45.0 + - + +
368B SER* 6.0 4.3 - - - +
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Residues in contact with TRP 352 (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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338B PHE* 3.8 28.5 - - + -
341B ILE* 3.8 25.1 - - + -
344B ALA* 3.9 22.9 - - + -
348B THR* 2.9 41.0 + - + +
349B ALA* 3.5 4.9 - - - +
351B MET* 1.3 86.7 - - + +
353B TYR* 1.3 64.0 + - - +
355B GLN* 3.2 25.5 + - - +
356B GLY 3.4 0.2 + - - -
357B PHE* 3.1 38.5 + + + +
363B ILE* 3.6 21.1 - - + -
367B ALA* 3.7 14.0 - - + +
368B SER 4.2 8.9 + - - +
369B LEU* 3.7 29.6 - - + -
373B GLN* 4.2 12.8 - - + -
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Residues in contact with TYR 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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330B GLU* 5.1 1.3 - - - +
331B SER* 3.8 39.2 + - - -
334B VAL* 3.6 22.4 - - + -
335B LEU* 3.9 16.4 - - + -
338B PHE* 4.2 2.4 - - + -
349B ALA 2.9 13.8 + - - +
350B GLN* 3.5 8.5 - - - +
351B MET 3.2 0.2 - - - -
352B TRP* 1.3 77.6 - - - +
354B GLN* 1.3 55.7 + - + +
356B GLY* 2.7 21.8 + - - -
357B PHE 3.8 6.1 - - - -
358B ARG* 3.0 57.3 + - - -
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Residues in contact with GLN 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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350B GLN 3.0 16.1 + - - +
351B MET* 3.2 9.6 + - + +
353B TYR* 1.3 75.5 - - + +
355B GLN* 1.3 60.6 + - + +
356B GLY* 3.0 6.9 + - - -
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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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351B MET* 3.0 31.7 + - + +
352B TRP* 3.4 27.6 - - - +
353B TYR 3.1 0.4 - - - -
354B GLN* 1.3 76.4 - - - +
356B GLY* 1.3 58.7 + - - +
357B PHE* 3.5 39.4 + - + -
366B GLN 5.2 2.6 + - - -
367B ALA* 5.3 2.0 - - - +
368B SER 5.6 1.5 + - - +
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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