Contacts of the helix formed by residues 305 - 316 (chain A) in PDB entry 1GC5
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 ASN 305 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304A LEU* 1.3 75.2 - - - +
306A GLU* 1.3 61.1 + - - +
307A VAL* 3.1 11.9 + - - +
308A GLU* 2.8 49.6 + - - +
309A LEU* 2.9 30.1 + - - +
351A PHE* 3.6 6.0 - - - -
352A HIS* 3.3 28.9 - - + +
353A THR* 5.5 0.4 - - - -
470A ADP 3.1 25.0 + - - +
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Residues in contact with GLU 306 (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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305A ASN* 1.3 75.5 - - - +
307A VAL* 1.3 69.1 + - + +
308A GLU 3.2 0.2 + - - -
309A LEU* 3.2 2.6 + - - +
310A ALA* 2.9 26.4 + - - +
325A VAL* 3.0 34.2 - - + +
326A LEU* 3.5 20.8 - - + +
328A GLY* 3.2 21.4 - - - +
333A VAL* 4.8 1.5 - - + +
351A PHE* 3.6 22.2 - - + -
352A HIS 4.2 1.0 + - - -
353A THR* 3.8 20.6 + - - +
356A TYR* 4.8 4.5 + - - -
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Residues in contact with VAL 307 (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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282A TYR* 3.9 28.7 - - + -
305A ASN* 3.1 13.0 + - - +
306A GLU* 1.3 77.7 - - + +
308A GLU* 1.3 58.6 + - + +
310A ALA* 3.6 2.3 + - - +
311A SER* 3.0 26.9 + - - -
326A LEU* 3.9 22.2 - - + +
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Residues in contact with GLU 308 (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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280A PHE* 3.3 28.6 - - + +
281A ALA* 3.6 6.9 - - - +
282A TYR* 3.5 30.9 + - + +
303A GLY 4.3 0.2 - - - +
304A LEU* 3.0 16.7 - - + -
305A ASN* 2.8 53.2 + - - +
307A VAL* 1.3 71.9 - - + +
309A LEU* 1.3 65.2 + - - +
311A SER* 2.6 25.9 + - - -
312A ILE* 3.0 13.0 + - - +
352A HIS* 5.2 0.7 - - - -
470A ADP 4.4 7.2 + - - -
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Residues in contact with LEU 309 (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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304A LEU* 4.3 27.0 - - + +
305A ASN 2.9 19.1 + - - +
306A GLU 3.7 3.1 - - - +
308A GLU* 1.3 74.4 - - - +
310A ALA* 1.3 64.1 + - - +
312A ILE* 3.1 8.2 + - + +
313A MET* 3.0 34.0 + - + +
325A VAL* 4.0 13.2 - - + -
333A VAL* 3.9 18.6 - - + +
336A ALA* 3.9 37.2 - - + +
337A MET* 4.3 8.1 - - + +
340A LEU* 4.6 9.2 - - + -
351A PHE* 3.9 20.9 - - + -
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Residues in contact with ALA 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A GLU 2.9 17.6 + - - +
307A VAL 3.7 3.6 - - - +
309A LEU* 1.3 77.3 - - - +
311A SER* 1.3 62.2 + - - +
313A MET* 2.9 6.8 + - - +
314A GLU* 2.9 21.5 + - - +
322A ALA* 3.4 36.3 - - + +
325A VAL* 4.1 7.1 - - + +
326A LEU* 3.5 22.7 - - + -
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Residues in contact with SER 311 (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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280A PHE* 5.5 2.9 - - - -
282A TYR* 3.9 23.3 - - - -
283A THR 5.4 1.6 + - - -
289A ARG* 3.2 41.7 + - - +
307A VAL 3.0 17.3 + - - -
308A GLU* 2.6 21.5 + - - +
310A ALA* 1.3 75.6 - - - +
312A ILE* 1.3 62.9 + - - +
314A GLU* 3.5 11.9 + - - +
315A ILE* 3.5 11.8 + - - +
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Residues in contact with ILE 312 (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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280A PHE* 3.9 37.9 - - + -
289A ARG* 4.9 1.1 - - - +
293A VAL* 4.4 15.5 - - + -
296A LEU* 4.9 1.8 - - + -
304A LEU* 3.5 32.5 - - + -
308A GLU 3.0 10.1 + - - +
309A LEU* 3.4 7.2 - - + +
311A SER* 1.3 81.9 + - - +
313A MET* 1.3 66.9 + - + +
315A ILE* 3.0 10.9 - - - +
316A ILE* 2.8 38.5 + - + +
340A LEU* 4.0 31.6 - - + -
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Residues in contact with MET 313 (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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309A LEU* 3.0 26.3 + - + +
310A ALA* 2.9 9.6 + - - +
312A ILE* 1.3 82.7 - - + +
314A GLU* 1.3 62.9 + - - +
316A ILE* 2.8 19.1 - - + +
318A ASP* 2.8 52.7 + - - +
321A LEU* 4.5 4.5 - - + -
322A ALA* 3.6 15.7 - - + +
325A VAL* 4.8 0.4 - - + -
336A ALA* 3.2 51.8 - - + +
339A VAL* 4.3 9.4 - - + -
340A LEU* 4.2 16.4 - - + +
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Residues in contact with GLU 314 (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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286A ARG* 2.5 36.5 + - - +
289A ARG* 2.7 34.5 + - - -
310A ALA 2.9 10.0 + - - +
311A SER* 3.7 10.7 - - - +
312A ILE 3.2 0.4 - - - -
313A MET* 1.3 75.6 - - - +
315A ILE* 1.3 61.6 + - - +
317A GLY* 2.7 16.8 + - - -
319A GLU* 3.1 28.6 - - + +
322A ALA* 4.0 8.9 - - + +
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Residues in contact with ILE 315 (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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286A ARG* 4.1 21.5 - - + +
289A ARG* 3.6 35.7 - - + +
290A GLU* 4.0 29.9 - - + +
293A VAL* 3.3 40.2 - - + -
311A SER 3.5 5.8 + - - +
312A ILE* 3.0 22.0 - - + +
314A GLU* 1.3 81.9 - - + +
316A ILE* 1.3 63.1 + - + +
317A GLY* 2.8 11.2 + - - -
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Residues in contact with ILE 316 (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 VAL* 5.9 4.9 - - + -
312A ILE* 2.8 23.2 + - + +
313A MET* 2.8 39.7 - - + +
315A ILE* 1.3 77.1 - - + +
317A GLY* 1.3 55.4 + - - +
318A ASP* 3.4 26.8 + - + +
339A VAL* 4.4 7.2 - - + -
340A LEU* 6.2 1.8 - - + -
343A GLU* 3.5 43.7 - - + +
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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