Contacts of the helix formed by residues 262 - 279 (chain U) in PDB entry 6QY3
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 LEU 262 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248U ILE 4.6 14.8 - - - +
249U PHE* 5.3 6.5 + - - +
251U GLU 4.6 6.9 + - - +
253U TYR* 5.2 9.3 - - + +
260U MET 4.0 0.2 + - - -
261U TYR* 1.3 75.2 - - - +
263U SER* 1.3 56.9 + - - +
265U ILE* 3.8 5.6 - - - +
266U VAL* 2.9 32.1 + - - +
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Residues in contact with SER 263 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187U MET* 6.4 1.6 - - - -
261U TYR* 3.2 6.3 - - - +
262U LEU* 1.3 79.4 - - - +
264U ASN* 1.3 56.8 + - - +
266U VAL* 3.5 4.0 + - - +
267U SER* 2.9 29.7 + - - -
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Residues in contact with ASN 264 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260U MET* 4.7 11.7 - - + -
261U TYR* 3.5 13.3 + - + +
262U LEU 3.4 0.4 - - - -
263U SER* 1.3 78.5 - - - +
265U ILE* 1.3 58.5 + - - +
267U SER* 3.3 6.8 + - - -
268U ASP* 2.9 30.8 + - - +
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Residues in contact with ILE 265 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253U TYR* 6.3 3.1 - - + -
255U TYR* 4.8 19.1 - - + -
260U MET* 5.0 5.0 - - + +
261U TYR 3.2 17.1 + - - +
262U LEU* 3.8 6.7 - - - +
264U ASN* 1.3 77.4 - - - +
266U VAL* 1.3 56.4 + - - +
268U ASP* 3.4 4.9 + - - +
269U TYR* 2.9 31.4 + - - +
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Residues in contact with VAL 266 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187U MET* 5.4 12.6 - - + -
188U PHE* 5.5 7.6 - - + -
191U GLU* 4.4 8.5 - - + +
262U LEU 2.9 17.3 + - - +
263U SER* 4.0 4.5 - - - +
265U ILE* 1.3 76.7 - - - +
267U SER* 1.3 57.2 + - - +
269U TYR* 3.9 5.9 - - - +
270U THR* 2.9 32.2 + - - -
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Residues in contact with SER 267 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191U GLU* 4.8 7.6 - - - -
263U SER 2.9 18.6 + - - -
264U ASN* 3.5 9.0 - - - -
265U ILE 3.2 0.2 - - - -
266U VAL* 1.3 78.3 - - - +
268U ASP* 1.3 57.8 + - - +
270U THR* 3.4 4.8 + - - -
271U LYS* 2.9 30.4 + - - +
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Residues in contact with ASP 268 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264U ASN 2.9 17.1 + - - +
265U ILE* 4.0 4.5 - - - +
267U SER* 1.3 77.4 - - - +
269U TYR* 1.3 56.2 + - - +
271U LYS* 3.4 5.2 + - - +
272U LYS* 2.9 31.2 + - - +
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Residues in contact with TYR 269 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265U ILE 2.9 17.5 + - - +
266U VAL* 3.9 6.7 - - - +
268U ASP* 1.3 77.2 - - - +
270U THR* 1.3 58.3 + - - +
272U LYS* 3.4 2.4 + - - +
273U VAL* 2.9 29.5 + - - +
285U PRO* 4.3 19.9 - - + +
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Residues in contact with THR 270 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188U PHE 5.6 0.4 - - - -
191U GLU* 3.9 28.5 - - - -
192U VAL* 5.0 2.9 - - - -
195U CYS* 5.5 3.8 - - - +
266U VAL 2.9 20.0 + - - -
267U SER 3.8 2.9 - - - -
269U TYR* 1.3 76.3 - - - +
271U LYS* 1.3 59.0 + - - +
273U VAL* 3.2 6.9 + - - +
274U ILE* 2.9 30.7 + - - +
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Residues in contact with LYS 271 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195U CYS* 6.1 2.0 - - - -
267U SER 2.9 18.4 + - - +
268U ASP* 3.8 6.5 - - - +
270U THR* 1.3 76.0 - - - +
272U LYS* 1.3 56.6 + - - +
274U ILE* 3.4 4.2 + - - +
275U LYS* 2.9 32.2 + - - +
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Residues in contact with LYS 272 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268U ASP 2.9 18.4 + - - +
269U TYR 3.8 3.8 - - - +
271U LYS* 1.3 76.1 - - - +
273U VAL* 1.3 56.6 + - - +
275U LYS* 4.2 4.2 - - - +
276U ALA* 2.9 31.9 + - - +
283U GLU 4.2 4.6 - - - +
285U PRO* 3.8 23.6 - - + -
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Residues in contact with VAL 273 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218U ILE* 5.9 6.7 - - + -
269U TYR 2.9 18.3 + - - +
270U THR* 3.2 7.8 + - - +
272U LYS* 1.3 75.2 - - - +
274U ILE* 1.3 60.4 + - - +
276U ALA* 3.4 4.1 + - - +
277U LEU* 2.9 29.6 + - - +
285U PRO* 5.2 3.5 - - + +
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Residues in contact with ILE 274 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195U CYS* 4.5 21.1 - - + -
197U CYS* 5.9 4.9 - - + -
270U THR 2.9 16.1 + - - +
271U LYS* 4.0 4.3 - - - +
273U VAL* 1.3 76.1 - - - +
275U LYS* 1.3 58.0 + - - +
277U LEU* 3.1 7.3 + - - +
278U ASN* 2.9 29.3 + - - +
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Residues in contact with LYS 275 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271U LYS 2.9 19.0 + - - +
272U LYS* 4.2 4.0 - - - +
274U ILE* 1.3 76.0 - - - +
276U ALA* 1.3 57.7 + - - +
278U ASN* 3.9 5.5 - - - +
279U GLN* 3.0 32.1 + - - +
282U GLU* 6.1 0.2 - - - -
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Residues in contact with ALA 276 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101U VAL* 5.6 0.2 - - - +
272U LYS 2.9 21.4 + - - +
273U VAL* 3.7 5.8 - - - +
275U LYS* 1.3 77.5 - - - +
277U LEU* 1.3 57.6 + - - +
279U GLN* 4.8 0.4 - - - -
280U LEU 3.0 8.1 + - - -
281U GLY* 2.6 32.8 + - - +
282U GLU* 4.4 12.1 - - - +
283U GLU 3.2 25.8 - - - +
284U ILE* 5.3 1.6 - - - -
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Residues in contact with LEU 277 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93U ARG 5.6 1.4 - - - +
97U TRP* 5.3 17.6 - - + +
98U LYS 5.9 0.2 + - - -
101U VAL* 5.1 11.7 - - + +
273U VAL 2.9 17.2 + - - +
274U ILE* 3.1 7.2 + - - +
276U ALA* 1.3 78.1 - - - +
278U ASN* 1.3 61.1 + - - +
280U LEU* 3.5 10.5 + - - +
281U GLY 5.0 0.2 - - - +
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Residues in contact with ASN 278 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93U ARG* 4.6 23.7 - - + +
274U ILE 2.9 16.1 + - - +
275U LYS* 4.1 5.6 - - - +
277U LEU* 1.3 76.8 - - - +
279U GLN* 1.3 59.5 + - - +
280U LEU* 3.3 2.1 + - - +
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Residues in contact with GLN 279 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275U LYS 3.0 18.2 + - - +
276U ALA 4.4 1.1 - - - +
278U ASN* 1.3 75.7 - - - +
280U LEU* 1.3 71.1 + - - +
281U GLY 3.6 0.7 - - - -
282U GLU* 4.5 18.9 + - + +
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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