Contacts of the helix formed by residues 311 - 319 (chain D) in PDB entry 1C2O
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 THR 311 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238D THR* 4.9 4.0 - - - +
303D VAL* 3.8 18.8 - - + +
310D ASP* 1.3 88.3 + - - +
312D PRO* 1.3 80.2 - - + -
313D GLU* 3.7 15.5 - - + +
314D ALA* 3.0 10.2 + - - +
315D LEU* 2.8 19.9 + - - +
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Residues in contact with PRO 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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211D MET* 5.5 0.7 - - + -
214D LEU* 4.5 8.3 - - + -
232D PRO* 2.9 46.7 - - + +
233D ASN* 3.8 6.7 - - + +
238D THR* 3.9 19.5 - - + +
303D VAL* 4.1 12.6 - - + -
308D LEU* 4.3 9.0 - - + -
310D ASP 3.5 3.1 - - - +
311D THR* 1.3 93.3 - - + +
313D GLU* 1.3 66.3 + - - +
315D LEU* 2.9 9.9 + - + -
316D ILE* 2.8 26.3 + - - +
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Residues in contact with GLU 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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233D ASN* 3.2 32.0 + - - +
311D THR* 3.1 13.1 - - + +
312D PRO* 1.3 81.2 - - - +
314D ALA* 1.3 66.8 + - - +
316D ILE* 3.2 8.1 - - + +
317D ASN* 2.9 24.2 + - + +
413D GLN* 3.7 30.7 + - - +
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Residues in contact with ALA 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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310D ASP* 3.5 31.2 - - + +
311D THR* 3.0 13.4 + - - +
313D GLU* 1.3 79.2 - - - +
315D LEU* 1.3 63.5 + - + +
317D ASN* 3.2 14.8 + - - +
318D THR* 3.0 26.7 + - + +
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Residues in contact with LEU 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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214D LEU* 3.4 53.2 - - + +
308D LEU* 4.8 5.4 - - + -
309D SER* 3.8 26.9 - - - +
310D ASP* 3.7 29.2 - - + +
311D THR 2.8 20.1 + - - +
312D PRO* 2.9 7.4 + - + +
314D ALA* 1.3 70.7 - - + +
316D ILE* 1.3 55.7 + - - +
317D ASN 2.9 4.1 + - - -
318D THR* 3.0 3.6 + - - +
319D GLY* 2.7 36.0 + - - +
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Residues in contact with ILE 316 (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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214D LEU* 4.1 20.4 - - + -
233D ASN* 4.1 21.1 - - + +
312D PRO 2.8 19.0 + - - +
313D GLU* 3.2 15.5 - - + +
315D LEU* 1.3 71.6 - - - +
317D ASN* 1.3 65.5 + - + +
318D THR 3.5 0.2 - - - -
321D PHE* 3.7 24.4 - - + -
413D GLN* 4.1 24.9 - - + +
414D LEU* 3.2 34.3 - - + -
417D ARG* 3.2 44.3 - - + +
418D LEU* 5.0 1.8 - - + -
421D GLN* 3.8 2.8 + - - -
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Residues in contact with ASN 317 (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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313D GLU* 2.9 19.8 + - + +
314D ALA* 3.4 13.0 - - - +
315D LEU 2.9 0.6 - - - -
316D ILE* 1.3 82.6 - - + +
318D THR* 1.3 76.4 + - - +
319D GLY 3.7 0.2 - - - -
417D ARG* 2.8 38.6 + - - +
421D GLN* 3.1 17.2 + - - +
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Residues in contact with THR 318 (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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314D ALA* 3.0 14.5 + - + +
315D LEU* 4.4 4.0 + - - +
317D ASN* 1.3 100.2 - - - +
319D GLY* 1.3 67.2 + - - +
320D ASP* 3.8 0.5 + - - +
421D GLN* 4.1 5.4 - - - -
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Residues in contact with GLY 319 (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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315D LEU* 2.7 23.1 + - - -
317D ASN 3.7 1.0 - - - -
318D THR* 1.3 75.8 - - - +
320D ASP* 1.3 61.7 + - - -
321D PHE* 3.4 19.5 - - - -
421D GLN* 2.8 27.5 - - - +
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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