Contacts of the helix formed by residues 294 - 301 (chain A) in PDB entry 4QGC
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 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A VAL* 3.3 19.4 + - + -
293A ALA* 1.3 71.3 - - - +
295A GLY* 1.3 62.1 + - - +
297A LEU* 3.3 11.1 + - - +
298A GLY* 3.0 19.6 + - - -
306A VAL* 4.3 6.0 - - + +
310A GLN* 3.0 46.8 + - + +
326A CYS* 4.3 8.1 - - - -
327A ALA 3.2 17.8 + - - +
328A THR* 3.1 15.9 + - - +
329A GLN* 3.0 17.1 + - - -
330A MET* 3.3 18.6 - - - -
347A ASP* 2.4 35.4 + - - -
351A ALA* 4.6 8.7 - - - +
342D ARG* 2.9 43.4 - - - +
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Residues in contact with GLY 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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178A ASP 5.6 2.9 - - - +
294A ARG* 1.3 73.7 - - - +
296A ASP* 1.3 61.6 + - - +
298A GLY* 3.2 14.4 + - - -
299A ILE* 3.7 10.8 + - - +
328A THR* 2.8 23.0 + - - -
329A GLN* 3.5 30.8 + - - -
342D ARG* 5.4 0.2 - - - -
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Residues in contact with ASP 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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178A ASP* 4.9 10.6 - - - +
210A ASN* 4.7 16.9 + - - +
244A PHE* 4.9 2.8 - - + -
272A GLU* 3.4 50.5 - - + +
293A ALA* 3.3 20.0 + - - +
295A GLY* 1.3 74.9 - - - +
297A LEU* 1.3 62.2 - - - +
299A ILE* 3.2 25.7 + - - +
300A GLU* 4.0 3.5 + - - +
328A THR* 4.0 11.6 - - - +
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Residues in contact with LEU 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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271A ILE 3.7 12.8 - - - +
272A GLU 3.4 27.4 - - - -
273A ASN* 3.6 17.9 - - - +
277A VAL* 4.4 5.4 - - + -
292A VAL* 3.8 26.7 - - + -
293A ALA 3.0 15.1 + - - +
294A ARG* 3.4 12.1 - - - +
295A GLY 3.2 0.2 - - - -
296A ASP* 1.3 77.7 - - - +
298A GLY* 1.3 57.0 + - - +
299A ILE 3.1 0.7 + - - -
300A GLU* 3.3 2.5 + - - +
301A ILE* 2.9 47.0 + - + +
306A VAL* 4.2 15.5 - - + -
309A ALA* 5.2 3.1 - - + -
310A GLN* 5.8 0.7 - - + +
313A MET* 3.9 17.0 - - + -
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Residues in contact with GLY 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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294A ARG 3.0 13.2 + - - -
295A GLY 3.2 7.4 + - - -
297A LEU* 1.3 76.4 - - - +
299A ILE* 1.3 62.2 + - - +
300A GLU 3.5 0.2 - - - -
301A ILE 3.1 19.7 - - - +
302A PRO* 5.2 0.5 - - - +
303A ALA* 6.3 0.2 - - - -
306A VAL* 3.9 10.3 - - - +
342D ARG* 4.6 12.1 - - - -
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Residues in contact with ILE 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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175A TYR* 3.8 33.8 + - + -
178A ASP 4.8 2.9 - - - +
179A GLY* 3.7 31.9 - - - +
210A ASN* 4.1 24.5 - - + +
212A PRO* 3.7 30.4 - - + +
295A GLY 3.9 10.8 - - - +
296A ASP* 3.3 18.6 - - - +
297A LEU 3.1 0.8 - - - -
298A GLY* 1.3 80.5 - - - +
300A GLU* 1.3 63.8 + - + +
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Residues in contact with GLU 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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211A LEU 4.9 1.4 - - - +
212A PRO* 3.7 43.8 - - + +
246A ARG* 5.6 1.6 + - - -
272A GLU 5.2 0.8 - - - +
273A ASN* 3.3 22.7 - - - +
274A HIS* 2.7 52.4 + - + +
275A GLU 4.4 0.7 + - - -
278A ARG* 4.9 1.9 + - - -
296A ASP 4.0 2.1 + - - +
297A LEU 3.3 4.4 + - - +
299A ILE* 1.3 82.1 - - + +
301A ILE* 1.3 63.1 - - + +
302A PRO* 3.8 5.9 - - - +
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Residues in contact with ILE 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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274A HIS* 4.5 18.8 - - + +
277A VAL* 4.1 20.0 - - + -
297A LEU* 2.9 29.3 + - + +
298A GLY* 3.1 19.3 - - - +
300A GLU* 1.3 83.2 - - + +
302A PRO* 1.3 83.3 - - + +
305A LYS* 3.7 20.9 - - + +
306A VAL* 3.4 18.0 - - + +
309A ALA* 4.6 6.5 - - + -
35D ILE* 3.7 29.6 - - + -
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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