Contacts of the helix formed by residues 296 - 303 (chain A) in PDB entry 1EXA
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 ARG 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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219A ARG* 3.4 15.5 - - - +
279A TYR* 4.2 4.6 + - - -
284A ASP* 2.8 53.4 + - - +
295A ASN* 1.3 74.9 - - - +
297A THR* 1.3 58.7 + - - +
299A MET* 3.2 2.8 + - - +
300A HIS* 2.9 27.2 + - - +
308A THR* 3.6 13.2 - - + +
309A ASP* 2.9 35.1 + - - +
312A PHE* 3.5 45.8 - - + +
313A ALA 5.4 0.2 - - - +
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Residues in contact with THR 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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215A SER 3.7 7.9 - - - +
216A ALA 3.8 8.4 + - - +
217A ASP 4.9 3.3 + - - -
218A HIS* 3.4 42.3 - - - +
219A ARG* 3.8 18.1 + - - +
295A ASN* 3.1 9.4 + - - -
296A ARG* 1.3 79.3 - - - +
298A GLN* 1.3 57.2 + - - +
300A HIS* 3.2 8.1 + - - +
301A ASN* 2.9 38.5 + - - +
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Residues in contact with GLN 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211A THR* 6.0 0.3 - - - -
212A THR* 2.9 39.5 + - - +
214A SER 2.9 28.1 + - - +
215A SER 3.7 8.5 - - - +
216A ALA* 3.5 13.3 - - - +
226A LEU* 3.6 15.9 - - + +
293A THR 4.3 2.8 - - - +
294A LEU* 3.6 19.7 - - + +
295A ASN* 2.8 42.8 + - - +
297A THR* 1.3 72.8 - - - +
299A MET* 1.3 61.5 + - - +
301A ASN 3.2 0.9 + - - -
302A ALA* 2.8 31.2 + - - +
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Residues in contact with MET 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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275A ILE* 4.1 3.4 - - + -
286A MET* 3.8 33.7 - - + -
288A PHE* 3.7 32.8 - - + -
294A LEU* 3.9 16.8 - - + +
295A ASN 2.8 18.4 + - - +
296A ARG 3.2 6.9 + - - +
298A GLN* 1.3 74.5 - - - +
300A HIS* 1.3 64.9 + - - +
302A ALA* 3.1 12.8 + - - +
303A GLY 3.5 0.2 + - - -
304A PHE* 3.3 58.3 + - + -
308A THR* 4.4 2.5 - - + -
312A PHE* 3.8 25.1 - - + -
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Residues in contact with HIS 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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219A ARG* 3.5 46.3 - - + +
220A VAL 2.9 24.2 - - - -
221A GLN* 4.7 6.5 - - - +
296A ARG 2.9 12.7 + - - +
297A THR 3.3 8.7 - - - +
298A GLN 3.2 0.2 - - - -
299A MET* 1.3 78.4 - - - +
301A ASN* 1.3 78.1 + - - +
303A GLY* 3.2 5.2 + - - -
305A GLY* 3.0 55.8 + - - +
306A PRO* 4.4 2.4 - - + +
308A THR* 3.0 21.0 + - + +
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Residues in contact with ASN 301 (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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215A SER* 2.9 33.5 + - - -
218A HIS 2.9 18.8 + - - -
219A ARG* 3.4 1.6 - - - -
220A VAL* 2.9 35.1 + - + +
222A LEU* 3.4 7.4 - - - +
223A ASP* 2.8 44.5 + - + +
226A LEU* 4.0 5.8 - - + -
297A THR* 2.9 18.0 + - - +
298A GLN 3.2 4.7 + - - +
300A HIS* 1.3 85.4 + - - +
302A ALA* 1.3 62.0 + - - +
303A GLY 3.2 2.7 - - - -
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Residues in contact with ALA 302 (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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222A LEU* 3.8 2.9 - - - -
226A LEU* 3.8 21.1 - - + -
227A TRP* 3.3 31.3 - - - +
230A PHE* 3.8 26.9 - - + -
294A LEU* 4.3 11.7 - - + -
298A GLN 2.8 16.8 + - - +
299A MET* 3.1 8.2 + - - +
301A ASN* 1.3 78.0 - - - +
303A GLY* 1.3 56.2 - - - +
304A PHE* 3.9 1.8 - - + -
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Residues in contact with GLY 303 (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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222A LEU* 3.7 15.9 - - - -
227A TRP* 4.6 0.2 - - - -
300A HIS 3.2 1.7 + - - -
301A ASN 3.2 4.2 - - - -
302A ALA* 1.3 81.1 - - - +
304A PHE* 1.3 61.6 + - - +
305A GLY 3.1 2.5 - - - -
396A ARG* 2.8 30.7 + - - +
400A LEU* 3.7 18.2 - - - +
450A 394 3.7 8.6 - - - +
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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