Contacts of the helix formed by residues 262 - 279 (chain i) in PDB entry 6QXT
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 i).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248i ILE 4.6 15.3 - - - +
249i PHE* 5.3 6.5 + - - +
251i GLU 4.6 6.9 + - - +
253i TYR* 5.2 9.5 - - + +
260i MET 4.1 0.4 + - - -
261i TYR* 1.3 74.5 - - - +
263i SER* 1.3 57.2 + - - +
265i ILE* 3.8 5.9 - - - +
266i VAL* 2.9 32.4 + - - +
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Residues in contact with SER 263 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187i MET* 6.4 1.6 - - - -
261i TYR* 3.2 6.3 - - - +
262i LEU* 1.3 81.0 - - - +
264i ASN* 1.3 56.2 + - - +
266i VAL* 3.8 4.4 - - - +
267i SER* 2.9 28.9 + - - -
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Residues in contact with ASN 264 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260i MET* 4.7 11.7 - - + -
261i TYR* 3.4 13.8 + - + +
262i LEU 3.4 0.4 - - - -
263i SER* 1.3 77.8 - - - +
265i ILE* 1.3 59.1 + - - +
267i SER* 3.5 7.0 - - - -
268i ASP* 2.9 30.5 + - - +
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Residues in contact with ILE 265 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253i TYR* 6.3 2.9 - - + -
255i TYR* 4.8 18.8 - - + -
260i MET* 4.9 5.1 - - + +
261i TYR 3.1 17.9 + - - +
262i LEU* 3.8 7.0 - - - +
264i ASN* 1.3 77.4 - - - +
266i VAL* 1.3 57.7 + - - +
268i ASP* 3.4 5.0 + - - +
269i TYR* 2.9 30.9 + - - +
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Residues in contact with VAL 266 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187i MET* 5.4 12.6 - - + +
188i PHE* 5.5 8.1 - - + -
191i GLU* 4.4 8.0 - - + +
262i LEU 2.9 17.9 + - - +
263i SER* 4.0 4.7 - - - +
265i ILE* 1.3 76.5 - - - +
267i SER* 1.3 58.0 + - - +
269i TYR* 3.9 5.7 - - - +
270i THR* 2.9 31.7 + - - -
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Residues in contact with SER 267 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191i GLU* 4.8 7.6 - - - -
263i SER 2.9 19.2 + - - -
264i ASN* 3.5 8.3 - - - -
265i ILE 3.2 0.2 - - - -
266i VAL* 1.3 76.3 - - - +
268i ASP* 1.3 57.4 + - - +
270i THR* 3.4 4.4 + - - -
271i LYS* 2.9 30.2 + - - +
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Residues in contact with ASP 268 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264i ASN 2.9 16.9 + - - +
265i ILE* 3.9 4.5 - - - +
267i SER* 1.3 76.7 - - - +
269i TYR* 1.3 58.0 + - - +
271i LYS* 3.8 5.7 - - - +
272i LYS* 2.9 31.4 + - - +
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Residues in contact with TYR 269 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265i ILE 2.9 18.1 + - - +
266i VAL* 3.9 6.7 - - - +
268i ASP* 1.3 77.6 - - - +
270i THR* 1.3 57.9 + - - +
272i LYS* 3.4 2.9 + - - +
273i VAL* 2.9 29.5 + - - +
285i PRO* 4.3 20.4 - - + +
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Residues in contact with THR 270 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188i PHE* 5.6 0.7 - - - -
191i GLU* 3.9 28.0 - - - -
192i VAL* 5.0 2.2 - - - -
195i CYS* 5.5 4.6 - - - +
266i VAL 2.9 19.0 + - - -
267i SER 3.8 3.4 - - - -
269i TYR* 1.3 77.3 - - - +
271i LYS* 1.3 57.9 + - - +
273i VAL* 3.2 7.2 + - - +
274i ILE* 2.9 30.1 + - - +
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Residues in contact with LYS 271 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195i CYS* 6.1 2.5 - - - -
267i SER 2.9 18.2 + - - +
268i ASP* 3.8 6.1 - - - +
270i THR* 1.3 76.8 - - - +
272i LYS* 1.3 58.0 + - - +
274i ILE* 3.4 4.0 + - - +
275i LYS* 2.9 33.2 + - - +
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Residues in contact with LYS 272 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268i ASP 2.9 18.2 + - - +
269i TYR 3.8 3.8 - - - +
271i LYS* 1.3 77.2 - - - +
273i VAL* 1.3 57.2 + - - +
275i LYS* 4.2 3.8 - - - +
276i ALA* 2.9 31.4 + - - +
283i GLU 4.2 4.5 - - - +
285i PRO* 3.8 24.0 - - + -
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Residues in contact with VAL 273 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218i ILE* 5.9 6.5 - - + -
269i TYR 2.9 18.3 + - - +
270i THR* 3.2 7.8 + - - +
272i LYS* 1.3 75.6 - - - +
274i ILE* 1.3 58.8 + - - +
276i ALA* 3.4 4.8 + - - +
277i LEU* 2.9 29.6 + - - +
285i PRO* 5.1 3.3 - - + +
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Residues in contact with ILE 274 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195i CYS* 4.5 21.1 - - + -
197i CYS* 5.9 4.9 - - + -
270i THR 2.9 15.6 + - - +
271i LYS* 4.0 4.3 - - - +
273i VAL* 1.3 77.7 - - - +
275i LYS* 1.3 56.9 + - - +
277i LEU* 3.1 7.0 + - - +
278i ASN* 2.9 30.5 + - - +
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Residues in contact with LYS 275 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271i LYS 2.9 19.4 + - - +
272i LYS* 4.2 4.0 - - - +
274i ILE* 1.3 76.6 - - - +
276i ALA* 1.3 57.5 + - - +
278i ASN* 3.5 5.9 + - - +
279i GLN* 3.0 32.4 + - - +
282i GLU* 6.2 0.2 - - - -
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Residues in contact with ALA 276 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272i LYS 2.9 21.9 + - - +
273i VAL* 3.7 5.2 - - - +
275i LYS* 1.3 78.6 - - - +
277i LEU* 1.3 56.4 + - - +
279i GLN* 4.8 0.7 - - - -
280i LEU 2.9 7.4 + - - -
281i GLY* 2.6 33.5 + - - +
282i GLU* 4.4 12.6 - - - +
283i GLU 3.2 24.9 - - - +
284i ILE* 5.3 2.0 - - - -
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Residues in contact with LEU 277 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93i ARG 5.6 1.1 - - - +
97i TRP* 5.3 18.6 - - + +
101i VAL* 5.1 12.2 - - + +
273i VAL 2.9 18.1 + - - +
274i ILE* 3.1 6.9 + - - +
276i ALA* 1.3 78.3 - - - +
278i ASN* 1.3 61.7 + - - +
280i LEU* 3.5 9.6 + - - +
281i GLY 5.0 0.4 - - - +
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Residues in contact with ASN 278 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93i ARG* 4.6 24.2 - - + +
274i ILE 2.9 15.8 + - - +
275i LYS* 4.1 6.5 - - - +
277i LEU* 1.3 76.5 - - - +
279i GLN* 1.3 59.1 + - - +
280i LEU* 3.3 2.2 + - - +
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Residues in contact with GLN 279 (chain i).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275i LYS 3.0 18.9 + - - +
276i ALA 4.4 0.9 - - - +
278i ASN* 1.3 75.0 - - - +
280i LEU* 1.3 71.4 + - - +
281i GLY 3.6 0.2 - - - -
282i GLU* 4.5 19.1 + - + +
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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