Contacts of the helix formed by residues 264 - 271 (chain Q) in PDB entry 5GJQ
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 PRO 264 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262Q ASN 4.0 2.0 - - - -
263Q THR* 1.4 69.2 - - - +
265Q GLU* 1.3 63.0 + - - -
266Q ASP 3.4 0.2 - - - -
267Q VAL* 3.1 12.3 + - + +
268Q GLN* 2.9 22.7 + - + +
291Q ALA* 3.9 13.7 - - + +
292Q GLN* 3.7 38.1 - - + +
295Q LYS* 2.7 43.8 + - + +
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Residues in contact with GLU 265 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263Q THR* 4.1 12.6 - - - -
264Q PRO* 1.3 77.2 - - - +
266Q ASP* 1.3 83.5 + - - +
268Q GLN* 3.0 12.4 + - - +
269Q ALA* 2.9 24.4 + - - +
295Q LYS* 4.1 10.6 - - - +
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Residues in contact with ASP 266 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258Q LYS* 2.4 51.1 + - + +
261Q LEU* 5.7 1.6 - - - +
263Q THR* 3.7 13.0 + - - +
264Q PRO 3.4 0.4 - - - -
265Q GLU* 1.3 94.1 - - - +
267Q VAL* 1.3 56.1 + - - +
269Q ALA* 3.1 13.9 - - + +
270Q LEU* 2.9 32.0 + - - +
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Residues in contact with VAL 267 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255Q LEU* 4.0 26.7 - - + +
258Q LYS* 3.8 18.2 - - + -
259Q ILE* 4.8 5.2 - - + -
263Q THR 3.5 17.0 - - - +
264Q PRO* 3.3 16.2 - - + +
265Q GLU 3.0 0.6 - - - -
266Q ASP* 1.3 74.0 - - - +
268Q GLN* 1.3 65.4 + - - +
269Q ALA 3.1 1.3 - - - -
270Q LEU* 2.9 11.8 + - - +
271Q VAL* 2.9 14.0 + - - +
287Q LEU 4.4 2.0 - - - +
288Q LYS* 4.3 20.9 - - + -
291Q ALA* 3.6 27.8 - - + -
292Q GLN* 6.4 0.2 - - + -
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Residues in contact with GLN 268 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264Q PRO* 2.9 12.4 + - + +
265Q GLU* 3.2 12.3 - - - +
267Q VAL* 1.3 75.5 - - - +
269Q ALA* 1.3 58.6 + - - +
271Q VAL* 2.8 31.1 + - - +
272Q SER* 5.2 0.3 - - - -
288Q LYS* 6.0 0.7 - - - +
292Q GLN* 6.1 2.9 - - - +
295Q LYS* 5.8 2.7 - - - +
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Residues in contact with ALA 269 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265Q GLU 2.9 8.3 + - - +
266Q ASP* 3.1 25.4 - - + +
268Q GLN* 1.3 77.0 - - - +
270Q LEU* 1.3 60.6 + - + +
271Q VAL 3.5 0.2 + - - -
272Q SER* 3.9 15.8 - - - -
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Residues in contact with LEU 270 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229Q TYR* 5.4 2.7 - - - +
251Q LEU* 4.8 13.3 - - + +
254Q MET* 4.6 17.9 - - + -
255Q LEU* 3.1 39.0 - - + -
258Q LYS* 4.8 8.5 - - + -
266Q ASP 2.9 20.7 + - - +
267Q VAL 2.9 2.4 + - - +
269Q ALA* 1.3 77.9 - - + +
271Q VAL* 1.3 58.8 + - - +
272Q SER* 3.1 8.0 + - - +
275Q LEU* 5.9 0.9 - - - +
276Q ALA* 4.4 16.3 - - - +
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Residues in contact with VAL 271 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255Q LEU* 5.7 3.8 - - + -
267Q VAL* 2.9 14.4 + - + +
268Q GLN* 2.8 21.9 + - - +
270Q LEU* 1.3 75.4 - - + +
272Q SER* 1.3 56.9 + - - +
277Q LEU* 4.6 9.9 - - + +
284Q THR* 4.7 15.3 - - + -
288Q LYS* 2.1 61.5 - - + +
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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