Contacts of the helix formed by residues 262 - 277 (chain C) in PDB entry 5G04
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 SER 262 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C GLU* 2.9 17.5 + - - -
58C LEU* 3.8 15.9 - - - +
60C PHE* 6.2 0.7 - - - -
61C SER* 3.0 28.5 + - - +
259C PHE 3.1 11.0 + - - -
260C SER 4.1 0.3 - - - +
261C LYS* 1.3 75.2 - - - +
263C SER* 1.3 60.7 + - - +
264C TYR* 3.3 9.9 + - - +
265C ILE* 3.5 20.6 + - - +
266C VAL* 2.9 24.7 + - - +
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Residues in contact with SER 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C GLU* 2.8 23.8 + - - +
261C LYS 3.4 4.7 + - - -
262C SER* 1.3 69.1 - - - +
264C TYR* 1.3 65.3 + - - -
266C VAL* 3.2 8.8 + - - +
267C SER* 2.9 23.0 + - - -
289C LEU* 3.9 7.4 - - - +
292C GLN* 5.0 9.0 - - - -
293C ASP* 4.2 15.0 + - - +
296C ARG* 3.5 27.5 + - - -
93P TYR* 5.1 3.2 + - - -
105P PHE* 5.6 3.1 - - - -
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Residues in contact with TYR 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C TRP* 3.4 51.7 - + + +
57C GLU* 3.7 16.7 + - + +
58C LEU* 4.3 7.2 - - + -
203C TRP* 4.5 2.4 - - - -
232C PHE* 4.2 20.7 + + - -
236C HIS* 4.3 17.3 + + - +
251C TYR* 3.6 23.1 + + - -
262C SER* 3.3 8.0 + - - +
263C SER* 1.3 79.9 + - - +
265C ILE* 1.4 66.8 + - + +
267C SER* 3.3 6.7 + - - -
268C GLN* 2.9 43.2 + - + +
296C ARG* 5.6 3.4 - - - +
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Residues in contact with ILE 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C LEU* 4.4 0.4 - - + -
232C PHE* 3.8 21.1 - - + -
251C TYR* 4.5 10.0 - - + +
254C LEU* 4.2 9.9 - - + +
255C ILE* 4.1 24.7 - - + -
259C PHE* 3.2 45.1 - - + +
260C SER* 5.5 1.6 - - - +
262C SER* 3.5 21.1 - - - +
264C TYR* 1.4 88.0 - - + +
266C VAL* 1.3 56.7 + - + +
268C GLN* 3.3 5.8 + - - +
269C ILE* 2.8 48.7 + - + +
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Residues in contact with VAL 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260C SER 4.0 14.6 - - - +
261C LYS 4.7 0.4 - - - +
262C SER 2.9 22.9 - - - +
263C SER* 3.2 7.6 + - - +
265C ILE* 1.3 74.2 - - + +
267C SER* 1.3 65.4 + - - +
269C ILE* 3.2 10.8 + - - +
270C ALA* 3.1 17.2 + - - +
285C ILE* 3.6 11.6 - - + +
288C GLU* 4.1 28.7 - - - +
289C LEU* 3.9 19.1 - - + -
292C GLN* 4.6 15.5 - - + +
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Residues in contact with SER 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263C SER 2.9 16.8 + - - -
264C TYR* 3.5 6.2 - - - -
266C VAL* 1.3 77.8 - - - +
268C GLN* 1.3 62.3 + - - +
270C ALA* 3.2 4.3 + - - +
271C VAL* 3.0 23.6 + - - +
286C PHE* 5.1 0.3 - - - -
289C LEU* 3.6 22.9 - - - +
296C ARG* 2.9 21.2 + - - -
299C ASN* 2.9 31.0 + - - +
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Residues in contact with GLN 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C HIS* 4.4 4.9 + - + +
239C THR* 3.1 40.2 + - + +
251C TYR* 3.0 57.9 + - + +
264C TYR* 2.9 35.9 + - + +
265C ILE* 3.3 5.4 + - - +
267C SER* 1.3 73.6 + - - +
269C ILE* 1.3 55.4 + - - +
271C VAL* 3.2 10.2 + - + +
272C ALA* 2.7 36.8 + - - +
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Residues in contact with ILE 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C LEU* 5.6 2.2 - - + +
251C TYR* 3.3 41.7 - - + -
255C ILE* 4.3 18.4 - - + -
265C ILE* 2.8 34.7 + - + +
266C VAL* 3.2 8.7 + - + +
268C GLN* 1.3 77.2 + - - +
270C ALA* 1.3 52.6 + - - +
272C ALA* 3.0 8.5 + - + +
273C TYR* 2.8 57.4 + - + -
285C ILE* 4.4 19.1 - - + -
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Residues in contact with ALA 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C VAL 3.1 5.7 + - - +
267C SER* 3.6 8.7 - - - +
269C ILE* 1.3 73.7 - - - +
271C VAL* 1.3 61.7 + - - +
273C TYR* 3.3 6.1 + - - +
274C HIS* 2.9 28.8 + - - +
282C ALA* 4.3 8.0 - - - +
285C ILE* 3.7 23.3 - - + +
286C PHE* 3.6 40.5 - - + +
289C LEU* 4.7 0.4 - - + -
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Residues in contact with VAL 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C THR* 5.0 7.6 - - + +
267C SER 3.0 15.6 + - - +
268C GLN* 3.5 11.4 - - + +
270C ALA* 1.3 74.1 - - - +
272C ALA* 1.3 57.4 - - - +
274C HIS* 3.3 9.0 + - + +
275C ASN* 2.9 44.5 + - - +
286C PHE* 4.5 2.0 - - + -
299C ASN* 3.7 33.9 - - + +
302C THR* 4.0 18.4 - - + +
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Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239C THR* 4.4 16.6 + - - +
244C ILE* 3.9 6.9 - - + +
247C ALA* 5.8 2.7 - - + -
248C LEU* 3.9 19.1 - - + -
251C TYR* 5.8 2.7 - - + -
268C GLN* 2.7 26.7 + - - +
269C ILE* 3.2 14.1 - - + +
271C VAL* 1.3 73.1 - - - +
273C TYR* 1.3 61.9 + - - +
275C ASN* 3.2 16.5 + - - +
276C ILE* 3.3 17.0 + - - +
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Residues in contact with TYR 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248C LEU* 3.6 36.6 - - + +
269C ILE* 2.8 47.2 + - + +
270C ALA* 3.8 1.3 - - - +
272C ALA* 1.3 70.5 - - - +
274C HIS* 1.3 61.9 + - - +
276C ILE* 3.2 20.0 - - + +
277C ARG 2.9 22.2 + - - -
278C ASP* 3.5 17.1 + - + -
281C LYS* 4.0 31.0 - - + -
282C ALA* 3.4 26.7 - - + -
285C ILE* 5.6 7.6 - - + -
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Residues in contact with HIS 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270C ALA 2.9 13.4 + - - +
271C VAL* 3.5 10.1 - - + +
273C TYR* 1.3 74.9 - - - +
275C ASN* 1.3 75.5 + - - +
277C ARG* 3.4 20.5 + - + +
279C ILE* 6.3 0.6 - - - +
282C ALA* 4.1 4.6 - - - +
286C PHE* 5.2 0.2 - - + -
302C THR* 3.6 27.1 + - - +
305C ASN* 4.5 24.5 + - + +
306C LEU* 4.1 29.6 - - + +
77R ASP* 5.8 9.3 + - + -
78R ARG* 5.8 5.6 - - + -
79R TYR* 5.4 8.9 - + - -
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Residues in contact with ASN 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239C THR* 3.8 19.8 + - - -
242C GLN* 3.0 34.6 + - - +
244C ILE* 4.0 15.8 - - + +
271C VAL* 2.9 26.7 + - - +
272C ALA* 3.2 9.8 + - - +
274C HIS* 1.3 88.2 - - - +
276C ILE* 1.3 58.3 + - - +
277C ARG* 3.5 11.4 + - - +
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Residues in contact with ILE 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244C ILE* 3.7 29.8 - - + -
248C LEU* 3.3 43.3 - - + -
272C ALA 3.4 9.6 - - - +
273C TYR* 3.2 24.9 - - + +
275C ASN* 1.3 73.0 - - - +
277C ARG* 1.3 75.1 + - - +
278C ASP* 3.9 21.1 - - + +
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Residues in contact with ARG 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273C TYR 2.9 6.7 + - - -
274C HIS* 3.6 18.8 - - + +
275C ASN 3.2 8.5 + - - +
276C ILE* 1.3 83.1 + - - +
278C ASP* 1.3 55.6 + - - +
279C ILE* 2.6 31.8 - - - +
434C ARG* 4.3 29.2 - - - +
465C VAL* 5.8 4.2 - - - +
74R PRO* 5.1 8.5 - - - +
75R GLY* 3.5 22.2 - - - +
76R GLY 4.5 0.2 - - - +
77R ASP* 2.3 62.3 + - + +
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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