Contacts of the helix formed by residues 315 - 328 (chain G) in PDB entry 6C3P
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 ALA 315 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311G LEU 3.7 3.4 + - - +
312G LEU* 2.6 29.3 + - + +
314G PHE* 1.3 70.1 - - - +
316G GLY* 1.3 61.8 + - - +
317G PRO* 3.6 0.7 - - - -
318G LEU* 3.7 24.5 - - + +
319G CYS* 3.6 15.2 + - - +
362G LEU* 4.4 3.4 - - - +
365G ALA* 6.1 4.3 - - + -
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Residues in contact with GLY 316 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312G LEU 4.2 0.2 + - - -
313G GLY* 2.9 15.6 + - - -
314G PHE 3.0 1.2 - - - -
315G ALA* 1.3 75.3 - - - +
317G PRO* 1.3 63.3 - - - +
319G CYS* 2.8 28.2 + - - +
320G ILE* 3.3 11.2 + - - +
362G LEU* 3.6 21.1 - - - +
366G LEU* 6.0 1.3 - - - -
585G ILE* 4.9 0.7 - - - -
1288G LEU* 4.7 8.1 - - - -
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Residues in contact with PRO 317 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G PHE* 3.3 18.2 - - + +
316G GLY* 1.3 89.1 - - - +
318G LEU* 1.3 61.8 + - + +
320G ILE* 2.8 26.6 + - + +
321G PHE* 2.9 14.4 + - - +
451G LEU* 5.8 2.2 - - + -
578G ALA* 4.2 13.9 - - + +
581G SER 4.7 0.4 - - - -
582G LEU* 3.8 41.1 - - + +
585G ILE* 3.6 29.6 - - + -
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Residues in contact with LEU 318 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314G PHE* 4.8 5.4 - - + +
315G ALA* 3.7 29.6 - - + +
316G GLY 3.1 0.2 + - - -
317G PRO* 1.3 77.3 - - - +
319G CYS* 1.3 62.3 + - - +
321G PHE* 3.4 7.0 + - + +
322G GLY* 2.9 20.8 + - - -
451G LEU* 4.1 30.1 - - + -
454G TYR* 6.5 0.4 - - + -
455G ILE* 3.9 28.5 - - + -
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Residues in contact with CYS 319 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315G ALA 3.6 4.9 + - - +
316G GLY 2.8 12.1 + - - +
318G LEU* 1.3 78.2 - - - +
320G ILE* 1.3 58.2 + - - +
323G ILE* 2.8 49.6 + - - +
358G LEU* 3.2 35.1 - - + +
359G ALA* 4.0 0.7 - - - -
362G LEU* 3.3 42.2 - - + -
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Residues in contact with ILE 320 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316G GLY 3.7 5.8 - - - +
317G PRO* 2.8 20.3 + - + +
319G CYS* 1.3 75.8 - - - +
321G PHE* 1.3 63.1 + - - +
323G ILE* 3.2 10.0 + - - +
324G VAL* 3.0 38.1 + - + +
362G LEU* 5.0 3.4 - - + -
577G PHE* 4.6 8.5 - - + -
578G ALA* 4.7 8.5 - - + -
581G SER* 3.6 24.0 - - - +
585G ILE* 5.3 0.2 - - + -
1281G GLY 4.7 0.4 - - - +
1284G LEU* 3.5 27.4 - - + -
1285G THR* 3.3 22.7 - - - +
1288G LEU* 3.8 26.5 - - + -
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Residues in contact with PHE 321 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317G PRO 2.9 11.4 + - - +
318G LEU* 3.7 11.2 - - + +
320G ILE* 1.3 75.7 - - - +
322G GLY* 1.3 66.5 + - - +
324G VAL* 3.2 5.1 + - - +
325G ASP* 2.9 51.3 + - + +
455G ILE* 4.8 22.0 - - + -
456G LEU* 4.4 12.6 - - + -
574G SER* 3.1 29.8 - - - -
575G VAL* 4.1 18.4 - - + -
578G ALA* 4.1 20.3 - - + +
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Residues in contact with GLY 322 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318G LEU 2.9 14.6 + - - -
319G CYS 3.7 2.7 - - - -
321G PHE* 1.3 76.5 - - - +
323G ILE* 1.3 64.1 + - - +
325G ASP* 2.6 16.5 - - - +
326G HIS* 2.3 41.4 + - - -
358G LEU* 4.1 9.2 - - - -
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Residues in contact with ILE 323 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319G CYS* 2.8 40.3 + - - +
320G ILE* 3.3 9.6 - - + +
322G GLY* 1.3 71.8 - - - +
324G VAL* 1.3 68.1 + - + +
326G HIS* 3.8 1.4 - - - +
327G LEU* 3.0 23.7 + - + +
355G ALA* 4.7 18.1 - - + +
358G LEU* 3.6 13.3 - - + +
359G ALA* 4.4 13.5 - - + -
362G LEU* 5.2 3.4 - - + -
1263G ALA* 5.2 4.9 - - + -
1267G ILE* 3.5 28.5 - - + -
1280G VAL* 4.6 3.6 - - + -
1284G LEU* 3.5 35.9 - - + -
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Residues in contact with VAL 324 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320G ILE* 3.0 23.6 + - + +
321G PHE* 3.2 0.6 + - - +
323G ILE* 1.3 81.3 - - + +
325G ASP* 1.3 58.7 + - - +
327G LEU* 3.2 8.6 + - - +
328G GLY* 2.9 23.4 + - - -
573G PRO 4.7 1.8 - - - -
574G SER* 3.5 38.6 - - - +
577G PHE* 5.8 2.9 - - + -
578G ALA* 6.2 0.2 - - + -
1277G ALA* 4.7 21.3 - - + +
1278G GLY* 5.2 3.8 - - - +
1280G VAL* 6.3 0.2 - - + -
1281G GLY* 4.3 25.6 - - - +
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Residues in contact with ASP 325 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321G PHE* 2.9 43.0 + - + +
322G GLY* 2.6 17.5 - - - +
324G VAL* 1.3 75.7 - - - +
326G HIS* 1.3 95.5 + - - +
328G GLY* 3.1 13.8 + - - +
329G LYS* 4.2 2.6 + - - +
574G SER* 4.4 12.1 - - - +
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Residues in contact with HIS 326 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322G GLY* 2.3 37.0 + - - +
323G ILE 3.9 2.0 - - - +
325G ASP* 1.3 95.8 + - - +
327G LEU* 1.3 61.6 + - - +
329G LYS 4.0 11.3 + - - -
354G ASN* 2.9 43.5 + - - +
355G ALA* 4.3 13.5 - - + -
358G LEU* 3.8 23.5 - - + +
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Residues in contact with LEU 327 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323G ILE* 3.0 14.6 + - + +
324G VAL* 3.4 10.3 - - - +
326G HIS* 1.3 73.2 - - - +
328G GLY* 1.3 67.3 + - - +
329G LYS* 2.8 12.6 + - - -
355G ALA* 5.4 2.6 - - + +
1267G ILE* 4.0 27.6 - - + +
1270G SER* 3.4 31.9 - - - +
1271G LEU* 4.4 25.0 - - + +
1277G ALA* 3.5 28.3 - - + -
1280G VAL* 4.6 3.6 - - + -
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Residues in contact with GLY 328 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324G VAL 2.9 14.0 + - - -
325G ASP* 3.1 11.6 + - - -
327G LEU* 1.3 77.3 - - - +
329G LYS* 1.3 73.3 + - - +
1277G ALA* 6.4 0.4 - - - -
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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
------------------------------------------------------------
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