Contacts of the helix formed by residues 302 - 316 (chain B) in PDB entry 2QKW
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 SER 302 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B HIS* 6.2 0.4 - - - -
220B GLU* 4.7 9.9 - - - -
221B LYS* 3.8 18.9 - - - +
224B VAL* 4.6 0.2 - - - -
300B ARG 3.9 0.2 + - - -
301B PRO* 1.3 72.9 - - - +
303B MET* 1.3 56.2 + - - +
304B GLY* 3.6 6.4 + - - -
305B ASP* 2.7 53.0 + - - -
306B VAL* 2.8 11.3 + - - -
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Residues in contact with MET 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ALA* 3.5 39.0 - - + -
152B LEU* 3.7 24.7 - - + -
153B HIS* 4.0 16.2 - - + +
156B HIS* 3.4 37.7 + - + +
220B GLU* 5.7 0.4 + - - -
223B ASP 5.1 0.2 - - - -
224B VAL* 3.8 21.6 - - + +
227B PHE* 3.9 30.7 - - + -
301B PRO 3.7 2.0 + - - -
302B SER* 1.3 70.9 - - - +
304B GLY* 1.3 53.0 + - - +
306B VAL* 3.5 10.8 - - + +
307B LEU* 2.7 35.9 + - - +
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Residues in contact with GLY 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B HIS* 3.5 30.1 - - - -
302B SER* 2.9 8.7 + - - -
303B MET* 1.3 78.2 - - - +
305B ASP* 1.3 61.5 + - - +
307B LEU* 3.3 10.9 - - - +
308B TRP* 3.1 19.4 + - - +
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Residues in contact with ASP 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PRO* 4.2 12.5 - - + +
302B SER* 2.7 34.9 + - - +
304B GLY* 1.3 68.1 - - - -
306B VAL* 1.3 66.6 + - - +
307B LEU 3.1 1.6 - - - -
308B TRP* 3.0 9.4 + - - +
309B LYS* 2.8 37.5 + - + +
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Residues in contact with VAL 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ALA* 4.8 0.2 - - + -
224B VAL* 4.4 0.9 - - + -
227B PHE* 3.7 35.0 - - + -
231B LEU* 4.8 0.9 - - + -
288B THR* 4.3 17.4 - - + +
292B CYS* 3.8 13.9 - - - -
301B PRO* 3.5 29.1 - - + +
302B SER 2.8 21.0 + - - +
303B MET* 3.5 23.1 - - + +
305B ASP* 1.3 70.1 - - - +
307B LEU* 1.3 62.6 + - - +
309B LYS* 3.4 3.0 + - - +
310B LEU* 3.0 31.1 + - + +
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 3.6 39.7 - - + +
149B ALA* 3.9 15.9 - - + -
150B ARG* 3.9 35.2 - - + +
153B HIS* 4.9 16.2 - - + +
303B MET 2.7 21.3 + - - +
304B GLY* 3.3 8.7 - - - +
306B VAL* 1.3 74.0 - - - +
308B TRP* 1.3 63.2 + - - +
310B LEU* 3.3 4.4 + - - +
311B GLU* 3.0 37.0 + - - +
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Residues in contact with TRP 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LYS* 5.4 5.2 - - - -
304B GLY 3.1 9.4 + - - +
305B ASP* 3.0 11.4 + - - +
307B LEU* 1.3 79.5 - - - +
309B LYS* 1.3 74.0 + - + +
311B GLU* 3.4 17.7 + - + +
312B TYR* 3.0 65.1 + + + +
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Residues in contact with LYS 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LYS* 3.4 31.1 - - - +
287B ASP* 5.6 0.9 - - - +
288B THR* 3.5 39.5 - - + +
291B LYS* 4.5 22.5 - - - +
301B PRO* 5.0 13.5 - - + -
305B ASP* 2.8 25.9 + - + +
306B VAL* 3.5 5.2 - - - +
308B TRP* 1.3 91.0 - - + +
310B LEU* 1.3 57.0 + - - +
312B TYR* 3.2 5.8 + - - +
313B ALA* 2.9 29.4 + - - +
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Residues in contact with LEU 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 3.9 11.9 - - + +
145B CYS* 3.8 27.1 - - + +
146B ILE* 3.7 15.8 - - + +
149B ALA* 4.3 5.6 - - + -
227B PHE* 3.8 23.8 - - + -
231B LEU* 3.8 9.4 - - + -
285B PHE* 3.6 39.5 - - + -
288B THR* 5.0 7.4 - - + -
306B VAL* 3.0 25.9 + - + +
307B LEU* 3.3 4.9 + - - +
309B LYS* 1.3 73.2 - - - +
311B GLU* 1.3 59.9 + - - +
313B ALA* 3.2 6.2 + - + +
314B LEU* 2.9 27.7 + - - +
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B ILE* 3.7 28.7 - - + +
150B ARG* 2.5 32.7 + - - -
307B LEU* 3.0 30.5 + - - +
308B TRP* 3.7 21.3 - - + +
310B LEU* 1.3 75.5 - - - +
312B TYR* 1.3 56.4 + - - +
314B LEU* 3.5 6.3 + - + +
315B ARG* 2.9 34.0 + - - +
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Residues in contact with TYR 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LYS* 4.5 14.4 - - + -
308B TRP* 3.0 55.3 + + + +
309B LYS* 3.5 4.7 - - - +
310B LEU 3.2 0.2 - - - -
311B GLU* 1.3 76.7 - - - +
313B ALA* 1.3 54.5 + - - +
315B ARG* 3.2 30.7 - - + +
316B LEU* 2.7 68.4 + - + +
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Residues in contact with ALA 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B LEU* 3.9 14.2 - - + +
281B SER* 3.3 32.4 + - - +
284B LYS* 3.8 24.5 - - + -
285B PHE* 4.3 8.1 - - + +
309B LYS 2.9 16.1 + - - +
310B LEU* 3.2 8.7 + - - +
312B TYR* 1.3 74.9 - - - +
314B LEU* 1.3 64.0 + - - +
316B LEU* 3.4 10.3 + - - +
317B GLN* 3.9 2.6 - - - +
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Residues in contact with LEU 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B GLU* 4.3 26.5 - - + +
142B LEU* 3.6 31.0 - - + +
143B GLU* 3.8 24.7 - - + +
146B ILE* 4.0 20.4 - - + -
310B LEU 2.9 12.6 + - - +
311B GLU* 3.6 9.0 - - + +
313B ALA* 1.3 71.5 - - - +
315B ARG* 1.3 67.8 + - - +
316B LEU 3.4 0.2 + - - -
317B GLN* 3.4 19.7 - - + +
318B GLU* 4.8 1.4 - - - +
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Residues in contact with ARG 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B GLU* 2.9 25.6 + - - +
312B TYR* 3.2 38.2 - - + +
314B LEU* 1.3 78.1 - - - +
316B LEU* 1.3 53.2 + - + +
317B GLN 2.6 15.9 + - - -
318B GLU* 3.2 37.0 + - + +
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Residues in contact with LEU 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ARG* 3.4 13.3 - - - -
280B GLU* 3.4 49.9 - - + +
281B SER* 3.3 24.3 + - - +
284B LYS* 4.0 15.7 - - + -
312B TYR* 2.7 61.0 + - + +
313B ALA* 3.8 6.7 - - - +
314B LEU 3.2 1.2 - - - -
315B ARG* 1.3 70.2 - - + +
317B GLN* 1.3 59.2 + - - +
318B GLU 3.9 1.6 - - - +
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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