Contacts of the helix formed by residues 376 - 381 (chain A) in PDB entry 2C10
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 376 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A HIS* 5.6 1.2 - - - -
246A GLU* 3.5 22.7 + - - -
265A PHE* 3.6 14.4 - - - -
374A GLY* 4.4 0.4 - - - -
375A ASN* 1.3 80.5 - - - +
377A PRO* 1.3 70.4 - - - +
378A ALA 3.3 1.0 + - - -
379A ALA* 3.5 5.6 + - - +
380A MET* 2.9 31.3 + - - +
498A ALA* 4.2 17.9 - - - +
499A PHE* 4.5 5.0 + - - +
501A PHE* 3.9 8.0 - - - -
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Residues in contact with PRO 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A TRP* 3.4 36.2 - - + -
246A GLU* 3.2 13.7 - - - +
265A PHE* 3.6 23.3 - - + -
270A TYR* 3.5 33.0 - - + +
375A ASN 4.8 0.4 - - - +
376A SER* 1.3 85.1 - - - +
378A ALA* 1.3 60.3 + - - +
380A MET* 3.5 8.0 - - + +
381A THR* 2.9 31.2 + - - +
553B TRP* 3.6 11.9 - - + -
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Residues in contact with ALA 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A THR* 3.9 20.4 - - + +
226A TRP* 4.0 21.2 - - + +
228A GLY* 5.1 5.4 - - - +
246A GLU* 3.0 30.4 + - + +
377A PRO* 1.3 79.1 - - - +
379A ALA* 1.3 60.3 + - - +
381A THR* 3.7 2.4 + - - -
382A THR* 2.5 31.2 + - - -
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Residues in contact with ALA 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A GLU* 5.0 0.8 + - - -
372A TYR* 3.3 24.9 - - + +
373A GLY 3.6 20.2 - - - +
374A GLY* 3.8 9.9 - - - -
375A ASN 4.9 0.2 - - - +
376A SER* 3.5 7.9 + - - +
378A ALA* 1.3 77.2 - - - +
380A MET* 1.3 64.7 + - - +
381A THR 3.0 1.6 + - - -
382A THR* 3.1 14.8 + - - -
498A ALA* 5.0 7.2 - - + -
518A THR* 3.8 20.2 - - + +
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Residues in contact with MET 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A TYR* 4.8 5.4 - - - -
372A TYR 4.1 2.6 - - - +
373A GLY* 4.6 0.8 - - - -
374A GLY 3.5 14.8 - - - +
375A ASN 4.9 3.4 - - - +
376A SER 2.9 19.9 + - - +
377A PRO* 3.5 12.3 - - - +
378A ALA 3.2 0.2 - - - -
379A ALA* 1.3 77.9 - - - +
381A THR* 1.3 58.6 + - + +
382A THR 3.6 0.2 - - - -
383A ARG* 3.7 18.9 + - - -
549B MET* 6.2 0.4 - - + -
552B PRO* 3.5 27.4 - - + -
553B TRP* 3.7 10.5 - - + -
559B LEU* 3.4 38.3 - - + +
560B GLN 5.0 1.7 - - - +
561B ARG* 3.2 48.8 - - - +
562B LEU 5.7 0.5 + - - -
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Residues in contact with THR 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A THR* 5.3 2.4 + - - -
214A ALA 3.7 5.9 - - - +
215A PRO* 3.8 11.6 + - - +
217A GLY 6.1 1.3 - - - -
218A LEU* 5.4 7.2 - - + -
226A TRP* 3.9 13.5 - - - -
377A PRO 2.9 12.0 + - - -
378A ALA* 3.7 2.4 + - - -
379A ALA 3.2 0.4 - - - -
380A MET* 1.3 78.6 - - - +
382A THR* 1.3 64.1 + - - +
383A ARG* 3.4 19.4 + - - +
621A MET* 5.5 0.5 - - - +
553B TRP* 3.6 32.5 - - + -
559B LEU* 3.9 20.4 - - + -
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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