Contacts of the helix formed by residues 284 - 294 (chain A) in PDB entry 2GC5
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 284 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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282A PRO* 5.3 6.7 - - + -
283A LEU* 1.3 78.1 - - - +
285A PRO* 1.3 74.0 - - + +
286A GLN* 3.4 9.7 + - - +
287A ASN* 3.0 37.4 + - - +
288A ILE* 3.1 28.1 + - - +
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Residues in contact with PRO 285 (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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249A ILE* 4.2 29.7 - - + +
283A LEU 4.7 1.1 - - - +
284A THR* 1.3 89.5 - - + +
286A GLN* 1.3 56.9 + - - +
288A ILE* 3.3 12.1 + - + +
289A ARG* 2.8 37.0 + - - +
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Residues in contact with GLN 286 (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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284A THR* 3.2 9.0 + - - +
285A PRO* 1.3 80.4 - - - +
287A ASN* 1.3 53.4 + - - +
289A ARG* 4.2 18.5 - - - +
290A GLN* 2.8 64.8 + - - +
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Residues in contact with ASN 287 (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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60A VAL 4.4 2.4 - - - +
63A ALA* 3.3 19.8 + - - +
64A SER* 3.6 28.5 - - - +
282A PRO 4.2 2.3 - - - +
283A LEU* 3.8 16.5 - - + -
284A THR* 3.0 42.1 + - - +
286A GLN* 1.3 75.7 - - - +
288A ILE* 1.3 58.8 + - - +
290A GLN* 3.4 18.6 + - - +
291A GLY* 2.9 26.9 + - - -
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Residues in contact with ILE 288 (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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60A VAL* 3.9 26.3 - - + +
249A ILE* 3.7 24.9 - - + -
252A LEU* 4.1 12.1 - - + -
269A ILE* 4.0 29.2 - - + -
273A LYS* 4.4 7.9 - - + -
283A LEU* 4.0 20.4 - - + +
284A THR 3.1 18.0 + - - +
285A PRO* 3.6 6.3 - - + +
287A ASN* 1.3 79.0 - - - +
289A ARG* 1.3 63.5 + - - +
291A GLY* 3.9 0.5 - - - -
292A LEU* 3.1 42.2 + - + +
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Residues in contact with ARG 289 (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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249A ILE* 3.9 17.6 - - - +
250A SER 2.9 21.8 + - - +
251A ASP* 2.9 30.7 + - - +
252A LEU* 3.6 22.9 - - + +
253A GLU 4.7 3.8 + - - +
285A PRO* 2.8 22.7 + - - +
286A GLN* 3.6 20.1 - - - +
288A ILE* 1.3 78.0 - - - +
290A GLN* 1.3 57.6 + - - +
292A LEU* 3.4 2.7 + - - +
293A ALA* 2.9 32.1 + - + +
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Residues in contact with GLN 290 (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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63A ALA* 4.3 13.2 + - + +
286A GLN* 2.8 50.4 + - - +
287A ASN* 3.5 26.5 - - - +
289A ARG* 1.3 73.0 - - - +
291A GLY* 1.3 56.0 + - - +
293A ALA* 3.1 7.9 + - - +
294A ALA* 2.8 39.6 + - + +
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Residues in contact with GLY 291 (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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59A HIS* 3.4 42.6 - - - +
60A VAL 4.2 2.9 - - - -
63A ALA* 3.7 5.7 - - - +
287A ASN 2.9 20.5 + - - -
288A ILE 3.9 0.9 - - - -
290A GLN* 1.3 72.3 - - - +
292A LEU* 1.3 61.4 + - - +
294A ALA* 3.4 4.8 + - - +
295A SER* 3.2 17.3 + - - -
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Residues in contact with LEU 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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56A ALA* 4.6 11.4 - - + -
59A HIS* 5.4 0.4 - - + -
60A VAL* 4.4 11.2 - - + +
240A PHE* 3.9 14.4 - - + -
252A LEU* 4.2 10.5 - - + -
253A GLU 3.7 12.8 - - - +
254A VAL* 4.3 8.1 - - + -
255A PRO* 3.4 10.2 - - - +
265A MET* 3.8 34.3 - - + +
269A ILE* 3.9 29.6 - - + -
288A ILE* 3.1 28.3 + - + +
289A ARG* 3.8 2.2 - - - +
291A GLY* 1.3 72.6 - - - +
293A ALA* 1.3 63.4 + - - +
295A SER* 2.5 27.1 + - - +
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Residues in contact with ALA 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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253A GLU* 3.7 13.2 + - + +
255A PRO* 4.0 14.9 - - - +
289A ARG* 2.9 21.9 + - + +
290A GLN* 3.5 8.3 - - - +
292A LEU* 1.3 78.0 - - - +
294A ALA* 1.3 59.2 + - + +
295A SER 3.3 1.1 + - - +
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Residues in contact with ALA 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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59A HIS* 4.2 6.8 - - - +
290A GLN* 2.8 20.3 + - + +
291A GLY* 3.8 5.4 - - - +
293A ALA* 1.3 70.7 - - - +
295A SER* 1.3 63.9 + - - +
296A HIS* 3.1 26.7 + - - +
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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