Contacts of the helix formed by residues 263 - 279 (chain L) 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 L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37L ASN* 5.4 0.7 - - - -
108L SER* 3.6 18.3 + - - -
262L TYR* 1.3 84.3 - - - +
264L GLN* 1.3 66.2 + - - +
265L ASP* 2.6 12.1 + - - +
267L ARG* 3.0 39.7 - - - +
445L GLU* 3.3 6.9 + - - -
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Residues in contact with GLN 264 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L ASN* 5.1 3.6 + - - +
37L ASN* 4.9 9.6 - - - +
259L VAL* 2.7 34.6 - - - +
260L MET 3.9 0.3 - - - -
261L GLY* 3.0 31.8 + - - +
262L TYR 3.1 3.6 + - - +
263L GLY* 1.3 73.6 - - - +
265L ASP* 1.3 52.7 - - - +
266L ASP 2.9 10.7 + - - -
267L ARG* 4.0 0.9 - - - -
268L ILE* 3.2 43.6 + - - +
343L VAL* 3.8 0.5 - - - +
437L LEU* 3.6 9.5 - - + +
445L GLU* 2.8 29.7 + - + +
446L ILE 4.4 0.2 - - - -
447L SER* 2.8 32.6 + - - -
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Residues in contact with ASP 265 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105L HIS* 3.2 5.9 + - - +
107L ASP 4.3 0.5 - - - +
108L SER* 3.5 16.2 + - - +
109L PRO* 5.1 2.5 - - + -
263L GLY 2.6 12.3 + - - +
264L GLN* 1.3 68.6 - - - +
266L ASP* 1.3 56.6 + - - +
267L ARG* 2.6 13.6 + - - -
296L GLU* 3.0 14.4 - - - +
342L ASP* 3.3 0.2 - - - +
343L VAL* 3.4 14.1 - - + +
437L LEU* 3.7 1.5 - - - +
440L MSE 3.0 13.5 - - - +
441L HIS* 3.0 11.9 + - + -
445L GLU* 3.0 21.5 + - - +
6023L MN 2.7 21.3 + - - -
6024L MN 2.5 26.9 + - - -
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Residues in contact with ASP 266 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L ALA* 3.2 4.6 - - - +
105L HIS* 2.4 68.3 + - + +
264L GLN 2.9 5.6 + - - -
265L ASP* 1.3 71.4 + - - +
267L ARG* 1.3 48.4 + - - -
268L ILE 2.9 5.6 - - - -
269L CYS* 2.7 9.7 + - - +
270L ALA* 2.6 34.7 + - - +
341L SER 2.7 25.6 - - - +
342L ASP* 2.9 18.3 - - - +
343L VAL* 3.3 15.6 - - - +
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Residues in contact with ARG 267 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L ASN* 4.9 2.3 + - - -
36L SER* 5.7 4.5 - - - +
37L ASN* 4.6 15.0 - - + +
40L THR* 3.6 11.1 + - - -
41L GLU* 3.3 43.6 + - - +
43L GLU* 4.3 6.9 - - - +
45L VAL* 4.1 25.0 - - + +
105L HIS 4.2 3.7 + - - -
106L ILE* 2.8 29.7 + - - +
107L ASP* 4.1 1.0 - - - +
108L SER* 3.6 29.2 + - - +
110L ARG* 6.0 1.0 - - - +
262L TYR* 4.1 5.5 + - - -
263L GLY* 3.0 32.5 - - - +
264L GLN* 4.8 0.4 - - - -
265L ASP 2.6 10.8 + - - +
266L ASP* 1.3 74.0 - - - +
268L ILE* 1.3 56.1 + - - +
270L ALA* 3.7 9.5 - - + +
271L TYR* 3.1 25.8 + - - +
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Residues in contact with ILE 268 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33L ASN* 3.9 22.4 - - - +
264L GLN* 3.2 43.3 + - - +
267L ARG* 1.3 77.2 - - - +
269L CYS* 1.3 67.9 + - - +
271L TYR* 3.4 2.1 + - - +
272L THR* 3.1 25.2 + - - +
343L VAL* 3.6 22.4 - - + -
435L VAL* 3.9 24.9 - - + -
437L LEU* 4.7 0.9 - - + -
447L SER* 3.7 11.2 - - - +
452L ILE* 3.7 36.1 - - + -
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Residues in contact with CYS 269 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104L ALA* 4.5 1.6 - - + -
266L ASP* 2.7 21.4 + - - +
268L ILE* 1.3 84.4 - - - +
270L ALA* 1.3 54.8 + - - +
271L TYR 3.0 2.2 - - - -
272L THR* 3.1 8.0 + - - -
273L SER* 2.7 41.6 + - - -
341L SER* 3.4 18.2 - - - +
342L ASP 4.0 3.1 - - - -
343L VAL* 4.1 8.1 - - - -
434L GLY* 3.4 33.0 - - - -
435L VAL* 3.7 12.3 - - - -
459L TYR* 3.8 5.9 - - - +
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Residues in contact with ALA 270 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45L VAL* 5.9 2.2 - - + -
49L ILE* 4.9 2.8 - - + +
104L ALA* 3.8 12.1 - - + +
105L HIS 4.4 1.6 - - - +
106L ILE* 4.0 17.7 - - + -
266L ASP 2.6 20.3 + - - +
267L ARG* 3.7 13.0 - - + +
269L CYS* 1.3 72.4 - - - +
271L TYR* 1.3 56.1 + - - +
273L SER* 2.8 16.8 + - - -
274L PHE* 3.3 14.9 + - - +
291L LEU* 3.9 26.9 - - + +
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Residues in contact with TYR 271 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29L ASP* 4.6 5.6 - - - -
32L LYS* 2.8 20.1 + - + +
33L ASN* 3.5 39.0 - - + +
36L SER* 3.7 27.8 - - - +
45L VAL* 6.4 0.2 - - + -
49L ILE* 5.4 9.2 - - + -
267L ARG 3.1 17.0 + - - +
268L ILE 3.6 5.4 - - - +
269L CYS 3.0 0.6 - - - -
270L ALA* 1.3 75.6 - - - +
272L THR* 1.3 66.8 + - + +
273L SER 3.1 0.7 - - - -
274L PHE* 2.7 47.7 + + + +
275L GLU* 2.7 46.3 + - + +
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Residues in contact with THR 272 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29L ASP* 5.2 3.6 - - - +
33L ASN* 6.1 0.2 - - + -
268L ILE* 3.1 14.5 + - + +
269L CYS* 3.1 12.3 + - - -
271L TYR* 1.3 82.7 - - + +
273L SER* 1.3 59.9 + - - +
275L GLU* 3.4 3.0 + - - +
276L ALA* 2.9 32.9 + - - +
435L VAL* 5.6 0.7 - - + -
452L ILE* 3.7 41.7 - - + +
455L THR* 3.6 6.9 - - + +
456L LYS* 3.9 26.7 - - + +
459L TYR* 3.2 14.0 - - - -
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Residues in contact with SER 273 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102L LEU* 3.9 25.0 - - - +
103L GLY 5.6 0.6 - - - -
104L ALA* 4.6 3.1 - - - +
269L CYS 2.7 24.4 + - - -
270L ALA* 2.8 21.5 + - - -
272L THR* 1.3 77.4 + - - +
274L PHE* 1.3 57.2 + - - +
276L ALA* 3.8 1.3 - - - +
277L MET* 3.0 30.1 + - - +
289L THR* 4.0 5.6 + - - +
291L LEU* 4.4 7.3 - - - +
341L SER* 5.2 2.9 - - - -
459L TYR* 3.3 23.8 - - - -
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Residues in contact with PHE 274 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49L ILE* 3.2 49.8 - - + -
52L ALA* 4.0 11.9 - - + -
53L GLU* 3.2 37.0 - - + -
87L MET* 3.3 20.6 - - + -
270L ALA 3.3 12.6 - - - +
271L TYR* 2.7 33.2 + + - +
273L SER* 1.3 80.7 + - - +
275L GLU* 1.3 59.8 + - + -
277L MET* 2.9 6.2 + - - +
278L LEU* 2.6 53.8 + - + +
289L THR* 5.1 1.8 - - - -
291L LEU* 5.1 3.1 - - + -
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Residues in contact with GLU 275 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L ASP* 3.5 6.4 - - - +
32L LYS* 3.0 35.2 + - - +
271L TYR* 2.7 50.1 + - + +
272L THR* 4.0 4.3 - - - +
274L PHE* 1.3 82.2 - - + +
276L ALA* 1.3 65.1 + - - +
278L LEU* 3.5 10.9 - - + +
279L GLU* 2.9 30.9 + - - +
456L LYS* 2.7 42.1 + - + +
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Residues in contact with ALA 276 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102L LEU* 4.8 2.5 - - + -
272L THR 2.9 18.3 + - - +
273L SER 3.8 3.1 - - - +
275L GLU* 1.3 79.1 - - - +
277L MET* 1.3 62.0 + - - +
279L GLU* 3.6 5.1 + - - +
280L MET* 3.4 23.5 + - - +
456L LYS* 4.0 14.9 - - + +
459L TYR* 3.7 27.6 - - + -
460L SER* 3.8 21.8 - - - +
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Residues in contact with MET 277 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57L TYR* 4.0 11.5 + - - +
87L MET* 3.2 42.2 - - + +
88L PHE 3.9 9.4 - - - +
89L LEU* 4.2 6.9 - - + +
102L LEU* 4.8 6.4 - - + +
273L SER 3.0 15.1 + - - +
274L PHE 2.9 4.8 + - - +
276L ALA* 1.3 75.8 - - - +
278L LEU* 1.3 63.7 + - - +
280L MET* 3.3 19.6 - - - +
287L CYS* 3.1 44.9 - - - +
288L ILE* 3.3 9.4 - - - -
289L THR* 3.0 28.7 - - - +
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Residues in contact with LEU 278 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52L ALA* 4.9 2.2 - - + -
53L GLU* 3.2 50.5 + - + +
55L SER* 4.9 9.6 - - - +
57L TYR* 4.5 6.6 + - - -
75L LYS* 5.3 6.4 + - - -
274L PHE* 2.6 40.3 + - + +
275L GLU* 3.5 10.5 - - + +
277L MET* 1.3 76.7 - - - +
279L GLU* 1.3 68.7 + - + +
280L MET 2.9 8.8 + - - +
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Residues in contact with GLU 279 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275L GLU* 2.9 24.4 + - - +
276L ALA* 3.8 5.8 - - - +
278L LEU* 1.3 79.7 - - + +
280L MET* 1.3 58.3 + - - +
281L LYS* 3.7 11.9 + - - +
456L LYS* 3.5 30.2 + - - -
460L SER* 5.5 6.3 - - - -
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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
------------------------------------------------------------
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