Contacts of the helix formed by residues 263 - 279 (chain C) in PDB entry 2GLJ
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 GLY 263 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASN* 5.4 1.1 - - - -
108C SER* 3.6 18.4 + - - -
262C TYR* 1.3 89.3 - - - +
264C GLN* 1.3 65.4 + - - +
265C ASP 2.6 11.1 + - - +
267C ARG* 3.0 36.0 - - - +
445C GLU* 3.3 7.7 + - - -
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Residues in contact with GLN 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ASN* 5.1 3.6 + - - +
37C ASN* 4.9 8.9 - - - +
259C VAL* 2.7 34.6 - - - +
260C MET 3.9 0.3 - - - -
261C GLY* 3.0 32.0 + - - +
262C TYR 3.2 3.2 + - - +
263C GLY* 1.3 71.7 - - - +
265C ASP* 1.3 54.7 + - - +
266C ASP 2.8 10.9 + - - -
267C ARG* 4.9 0.7 - - - -
268C ILE* 3.2 43.3 + - - +
343C VAL* 3.8 0.3 - - - +
437C LEU* 3.6 9.0 - - + +
445C GLU* 2.8 33.3 + - + +
447C SER* 2.8 31.6 + - - -
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Residues in contact with ASP 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105C HIS* 3.2 6.4 + - - -
107C ASP 4.3 0.3 - - - +
108C SER* 3.4 17.7 + - - +
109C PRO* 5.1 2.2 - - + -
263C GLY 2.6 9.6 + - - +
264C GLN* 1.3 68.2 - - - +
266C ASP* 1.3 56.6 + - - +
267C ARG* 2.7 14.1 + - - +
296C GLU* 3.0 21.2 - - - +
342C ASP* 3.3 0.2 - - - +
343C VAL* 3.4 13.8 - - + +
437C LEU* 3.7 2.0 - - - +
440C MSE 3.0 19.8 - - - +
441C HIS* 3.0 19.8 + - + -
445C GLU* 3.0 20.8 + - - +
6005C MN 3.3 0.2 + - - -
6006C MN 2.4 26.1 + - - -
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Residues in contact with ASP 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ALA* 3.2 5.0 - - - +
105C HIS* 2.4 67.8 + - + +
264C GLN 2.8 5.0 + - - -
265C ASP* 1.3 71.7 + - - +
267C ARG* 1.3 48.4 + - - +
268C ILE 2.8 5.8 - - - -
269C CYS* 2.7 9.2 + - - +
270C ALA* 2.6 33.8 + - - +
341C SER 2.7 25.8 - - - +
342C ASP* 2.9 17.4 - - - +
343C VAL* 3.3 15.8 - - - +
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Residues in contact with ARG 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ASN* 4.9 2.6 + - - +
36C SER* 5.7 4.3 - - - +
37C ASN* 4.6 13.9 - - + +
40C THR* 3.6 11.0 + - - -
41C GLU* 3.3 43.4 + - - +
43C GLU* 4.3 6.5 - - - +
45C VAL* 4.1 25.0 - - + +
105C HIS 4.2 4.2 + - - -
106C ILE* 2.8 30.1 + - - +
107C ASP* 4.1 0.8 - - - +
108C SER* 3.6 29.2 + - - +
110C ARG* 6.0 0.8 - - - +
262C TYR* 4.1 4.9 + - - -
263C GLY* 3.0 33.1 - - - +
264C GLN* 4.9 0.2 - - - -
265C ASP 2.7 10.3 + - - +
266C ASP* 1.3 72.9 - - - +
268C ILE* 1.3 57.1 + - - +
270C ALA* 3.7 10.4 - - + +
271C TYR* 3.1 25.5 + - - +
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Residues in contact with ILE 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C ASN* 3.9 22.9 - - - +
264C GLN* 3.2 46.0 + - - +
267C ARG* 1.3 78.2 - - - +
269C CYS* 1.3 67.5 + - - +
271C TYR* 3.4 2.4 + - - +
272C THR* 3.1 24.1 + - - +
343C VAL* 3.6 22.0 - - + -
435C VAL* 3.9 24.2 - - + -
437C LEU* 4.7 0.9 - - + -
447C SER* 3.8 10.3 - - - +
452C ILE* 3.7 35.0 - - + -
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Residues in contact with CYS 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104C ALA* 4.5 1.6 - - + -
266C ASP* 2.7 23.4 + - - +
268C ILE* 1.3 86.1 - - - +
270C ALA* 1.3 54.0 + - - +
271C TYR 3.0 2.0 - - - -
272C THR* 3.0 7.8 + - - -
273C SER* 2.6 42.8 + - - -
341C SER* 3.4 17.9 - - - +
342C ASP 4.0 3.1 - - - -
343C VAL 4.0 7.4 - - - -
434C GLY* 3.4 33.2 - - - -
435C VAL* 3.8 11.9 - - - -
459C TYR* 3.8 6.4 - - - +
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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
----------------------------------------------------------
45C VAL* 5.9 2.5 - - + -
49C ILE* 4.9 3.2 - - + +
104C ALA* 3.8 12.3 - - + +
105C HIS 4.4 1.3 - - - +
106C ILE* 4.0 17.7 - - + -
266C ASP 2.6 19.4 + - - +
267C ARG* 3.7 13.2 - - + +
269C CYS* 1.3 72.8 - - - +
271C TYR* 1.3 58.3 + - - +
273C SER* 2.8 16.7 + - - -
274C PHE* 3.3 13.7 + - - +
291C LEU* 3.9 26.3 - - + +
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Residues in contact with TYR 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ASP* 4.6 4.9 - - - -
32C LYS* 2.8 20.0 - - + +
33C ASN* 3.5 39.3 - - + +
36C SER* 3.7 28.0 - - - +
45C VAL* 6.4 0.7 - - + -
49C ILE* 5.4 9.6 - - + -
267C ARG 3.1 16.6 + - - +
268C ILE 3.6 5.4 - - - +
269C CYS 3.0 0.6 - - - -
270C ALA* 1.3 74.8 - - - +
272C THR* 1.3 65.4 + - + +
273C SER 3.1 1.3 - - - -
274C PHE* 2.7 47.6 + + + +
275C GLU* 2.7 46.9 + - + +
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Residues in contact with THR 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ASP* 5.2 3.4 - - - +
268C ILE* 3.1 14.6 + - + +
269C CYS* 3.0 11.8 + - - -
271C TYR* 1.3 85.2 - - + +
273C SER* 1.3 69.5 + - - +
275C GLU* 3.4 2.4 + - - +
276C ALA* 2.9 26.5 + - - +
435C VAL* 5.6 0.9 - - + -
452C ILE* 3.7 41.7 - - + +
455C THR* 3.6 6.1 - - + +
456C LYS* 3.9 28.0 - - + +
459C TYR* 3.2 14.8 - - - -
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Residues in contact with SER 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LEU* 3.8 25.5 - - - +
103C GLY 5.6 0.2 - - - -
104C ALA* 4.6 3.5 - - - +
269C CYS 2.6 23.9 + - - -
270C ALA* 2.8 22.2 + - - -
272C THR* 1.3 77.9 + - - +
274C PHE* 1.3 55.9 + - - +
276C ALA* 3.8 0.9 - - - +
277C MET* 3.0 29.8 + - - +
289C THR* 4.1 5.4 + - - +
291C LEU* 4.4 7.4 - - - +
341C SER* 5.2 3.1 - - - -
459C TYR* 3.3 23.3 - - - -
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Residues in contact with PHE 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 3.2 52.0 - - + -
52C ALA* 4.0 11.4 - - + -
53C GLU* 3.2 36.6 - - + -
87C MET* 3.4 20.4 - - + -
270C ALA 3.3 12.6 - - - +
271C TYR* 2.7 32.3 + + - +
273C SER* 1.3 79.2 + - - +
275C GLU* 1.3 60.2 + - + -
277C MET* 2.9 6.9 + - - +
278C LEU* 2.6 54.2 + - + +
289C THR* 5.1 2.0 - - - -
291C LEU* 5.1 3.1 - - + -
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Residues in contact with GLU 275 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C ASP* 3.5 6.7 - - - +
32C LYS* 3.0 33.6 + - - +
271C TYR* 2.7 54.4 + - + +
272C THR* 4.0 4.5 - - - +
274C PHE* 1.3 81.7 - - + +
276C ALA* 1.3 64.6 + - - +
278C LEU* 3.0 9.6 + - + -
279C GLU* 2.8 31.8 + - - +
456C LYS* 2.7 43.0 + - + +
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Residues in contact with ALA 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LEU* 4.8 2.7 - - + -
272C THR 2.9 18.5 + - - +
273C SER 3.8 3.1 - - - +
275C GLU* 1.3 79.4 - - - +
277C MET* 1.3 61.3 + - - +
279C GLU* 3.6 6.4 + - - +
280C MET* 3.4 23.5 + - - +
456C LYS* 4.0 14.5 - - + +
459C TYR* 3.7 28.0 - - + -
460C SER* 3.8 18.9 - - - +
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Residues in contact with MET 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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57C TYR* 3.9 11.0 + - - +
87C MET* 3.2 46.7 - - + +
88C PHE 3.9 9.4 - - - +
89C LEU* 4.4 6.4 - - - +
102C LEU* 4.8 6.0 - - + +
273C SER 3.0 14.4 + - - +
274C PHE 2.9 4.1 + - - +
276C ALA* 1.3 76.0 - - - +
278C LEU* 1.3 64.4 + - - +
280C MET* 3.3 19.1 - - - +
287C CYS* 3.1 46.2 - - - +
288C ILE* 3.4 8.7 - - - -
289C THR* 3.1 25.1 - - - +
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Residues in contact with LEU 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA* 4.9 2.0 - - + -
53C GLU* 3.1 49.9 - - + +
55C SER* 4.9 8.7 - - - +
57C TYR* 4.5 6.4 + - - -
75C LYS* 5.3 6.2 + - - -
274C PHE* 2.6 42.2 + - + +
275C GLU* 3.5 9.2 - - + +
277C MET* 1.3 71.7 - - - +
279C GLU* 1.3 68.1 - - + +
280C MET 2.9 13.4 + - - +
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Residues in contact with GLU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C GLU* 2.8 23.2 + - - +
276C ALA* 3.9 6.1 - - - +
278C LEU* 1.3 80.8 - - + +
280C MET* 1.3 58.2 + - - +
281C LYS* 3.7 11.9 + - - +
456C LYS* 3.5 30.2 + - - -
460C SER* 5.6 6.4 - - - -
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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
------------------------------------------------------------
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