Contacts of the helix formed by residues 291 - 300 (chain A) in PDB entry 2CIA
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 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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289A ASN 4.5 5.2 - - - +
290A VAL* 1.3 77.4 - - - +
292A ARG* 1.3 65.7 + - - +
293A HIS* 3.6 7.7 + - - +
294A GLN* 3.0 41.9 + - - +
295A ALA* 2.9 21.8 + - - +
311A ARG* 4.1 1.8 - - - -
314A GLU* 3.6 28.3 - - + +
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Residues in contact with ARG 292 (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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291A THR* 1.3 71.7 - - - +
293A HIS* 1.3 58.0 + - - +
295A ALA* 3.1 3.1 + - - +
296A GLU* 2.9 34.0 + - + +
311A ARG* 3.7 21.2 - - - +
314A GLU* 2.8 20.6 + - - +
332A HIS* 3.8 34.9 - - + +
471L ACE 5.8 0.2 - - - +
472L HIS* 3.7 34.6 - - + +
473L ILE* 2.9 36.6 + - - +
474L PTR 2.8 48.6 + - - +
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Residues in contact with HIS 293 (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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291A THR* 3.2 7.6 + - - +
292A ARG* 1.3 79.1 - - - +
294A GLN* 1.3 72.2 + - + +
296A GLU* 3.3 9.6 + - + +
297A CYS* 3.0 47.1 + - - -
314A GLU* 4.5 0.8 + - - -
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Residues in contact with GLN 294 (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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289A ASN 4.3 1.4 - - - +
290A VAL* 3.3 21.9 - - + +
291A THR* 3.0 46.8 + - - +
293A HIS* 1.3 84.2 - - + +
295A ALA* 1.3 56.8 + - - +
297A CYS* 3.3 6.5 + - - +
298A ALA* 2.9 30.4 + - - +
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Residues in contact with ALA 295 (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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290A VAL* 4.6 3.9 - - + +
291A THR 2.9 13.6 + - - +
292A ARG 3.4 8.1 - - - +
294A GLN* 1.3 73.6 - - - +
296A GLU* 1.3 65.2 + - - +
298A ALA* 3.9 1.0 - - - +
299A LEU* 2.9 32.4 + - - +
309A LEU* 4.1 19.5 - - + -
311A ARG* 3.7 25.1 - - - +
323A SER* 4.0 13.2 - - - +
332A HIS* 4.6 2.0 - - + -
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Residues in contact with GLU 296 (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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292A ARG* 2.9 25.7 + - + +
293A HIS* 3.3 12.5 + - + +
295A ALA* 1.3 75.7 - - - +
297A CYS* 1.3 66.3 + - - +
299A LEU* 3.9 2.0 - - - +
300A ASN* 3.0 36.5 + - - +
329A LYS* 5.1 7.8 + - - +
330A ASN* 2.9 38.0 + - - +
332A HIS* 2.8 31.2 + - - +
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Residues in contact with CYS 297 (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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293A HIS* 3.0 48.6 + - - +
294A GLN* 3.7 5.8 - - - +
296A GLU* 1.3 81.3 - - - +
298A ALA* 1.3 56.5 + - - +
300A ASN* 3.3 4.7 + - - +
301A GLU* 2.9 32.6 + - - +
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Residues in contact with ALA 298 (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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287A TYR* 5.2 6.1 - - + -
294A GLN 2.9 17.7 + - - +
295A ALA* 3.9 5.8 - - - +
297A CYS* 1.3 73.4 - - - +
299A LEU* 1.3 66.4 + - - +
301A GLU* 4.6 4.0 - - - -
302A ARG* 3.0 36.6 + - - +
309A LEU* 4.8 2.9 - - + -
379A LEU* 3.7 19.3 - - + +
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Residues in contact with LEU 299 (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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295A ALA 2.9 23.9 + - - +
296A GLU 3.9 3.1 - - - +
298A ALA* 1.3 75.3 - - - +
300A ASN* 1.3 61.5 + - - +
303A GLY* 2.8 30.5 + - - +
307A ASP 3.7 24.9 - - - +
308A PHE* 4.1 7.0 - - - -
309A LEU* 4.4 7.4 - - + -
323A SER* 3.8 39.0 - - - +
324A LEU 4.0 11.7 - - - +
325A LYS* 3.6 15.0 - - + +
330A ASN* 4.1 18.4 - - + +
332A HIS* 5.2 1.3 - - + -
379A LEU* 3.9 21.3 - - + +
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Residues in contact with ASN 300 (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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296A GLU* 3.0 26.4 + - - +
297A CYS* 3.9 4.2 - - - +
299A LEU* 1.3 77.7 - - - +
301A GLU* 1.3 60.3 + - - +
303A GLY 4.5 5.5 - - - +
325A LYS* 2.7 33.1 + - - +
330A ASN* 3.0 23.5 + - - +
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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