Contacts of the helix formed by residues 297 - 314 (chain B) in PDB entry 2QU7
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 297 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B VAL* 3.9 15.3 - - + -
295B SER 4.3 0.2 - - - +
296B GLN* 1.3 83.9 - - + +
298B VAL* 1.3 51.7 + - - +
299B LYS 3.5 2.2 - - - -
300B GLU* 3.4 22.0 + - + +
301B MET* 2.8 35.9 + - + +
323B LEU* 3.8 26.9 - - + -
324B SER 3.4 28.0 - - - +
325B THR* 4.3 0.7 - - - -
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Residues in contact with VAL 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 3.7 34.8 - - + +
80B GLU* 4.0 29.8 - - + +
81B VAL* 3.9 26.3 - - + +
84B GLU* 4.1 5.4 - - + +
296B GLN* 2.8 21.1 + - + +
297B PRO* 1.3 68.9 - - - +
299B LYS* 1.3 69.4 + - + +
301B MET* 3.7 3.1 - - - +
302B GLY* 2.9 26.9 + - - -
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Residues in contact with LYS 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU* 3.3 38.4 + - + +
297B PRO 3.5 0.2 - - - -
298B VAL* 1.3 87.1 - - + +
300B GLU* 1.3 59.6 + - - +
302B GLY* 3.2 2.9 + - - -
303B GLN* 2.9 45.4 + - - +
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B PRO* 3.4 24.3 + - + +
299B LYS* 1.3 78.1 - - - +
301B MET* 1.3 56.7 + - - +
303B GLN* 3.3 12.6 + - + +
304B VAL* 2.8 48.0 + - + +
323B LEU* 3.6 25.8 - - + +
324B SER 5.7 0.3 + - - -
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Residues in contact with MET 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B PHE* 4.1 32.5 - - + -
81B VAL* 4.3 7.2 - - + -
146B LEU* 4.1 25.6 - - + -
147B ASP* 5.1 2.7 - - - -
158B ILE* 3.5 32.9 - - + +
159B THR* 5.2 3.6 - - - -
160B VAL* 3.9 28.5 - - + -
296B GLN* 4.5 0.2 - - - +
297B PRO* 2.8 28.6 + - + +
298B VAL* 3.7 5.8 - - - +
300B GLU* 1.3 72.2 - - - +
302B GLY* 1.3 53.0 + - - +
304B VAL 3.4 0.2 + - - -
305B ALA* 2.8 37.5 + - - +
323B LEU* 3.8 14.5 - - + +
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Residues in contact with GLY 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B VAL* 4.1 5.3 - - - +
84B GLU* 3.8 11.7 - - - -
85B ILE* 3.5 30.1 - - - +
298B VAL 2.9 15.3 + - - -
299B LYS 3.6 3.4 - - - -
301B MET* 1.3 72.4 - - - +
303B GLN* 1.3 59.5 + - - +
306B ALA* 3.1 31.4 + - - +
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Residues in contact with GLN 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B GLU* 3.6 20.6 + - - +
88B GLU* 4.7 15.4 - - + +
299B LYS* 2.9 34.7 + - - +
300B GLU* 3.6 11.5 - - - +
302B GLY* 1.3 74.8 - - - +
304B VAL* 1.3 63.7 - - + +
306B ALA* 3.6 5.2 + - - +
307B LYS* 3.1 39.1 + - - +
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Residues in contact with VAL 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158B ILE* 3.6 22.7 - - + -
300B GLU* 2.8 40.9 + - + +
301B MET* 4.7 0.2 - - - -
303B GLN* 1.3 75.7 - - + +
305B ALA* 1.3 53.8 + - - +
307B LYS* 3.2 9.1 + - + +
308B MET* 2.7 47.7 + - + +
321B ILE* 4.1 18.8 - - + -
323B LEU* 4.9 5.2 - - + -
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Residues in contact with ALA 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 4.0 20.6 - - + -
124B ILE* 5.0 2.2 - - + -
144B MET* 3.9 23.5 - - + +
146B LEU* 4.2 8.3 - - + -
158B ILE* 4.2 3.5 - - + +
301B MET 2.8 21.2 + - - +
302B GLY 4.0 2.9 - - - +
303B GLN 3.4 0.2 - - - -
304B VAL* 1.3 72.6 - - - +
306B ALA* 1.3 52.9 + - - +
308B MET* 3.2 9.6 + - - +
309B ILE* 2.7 39.9 + - - +
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Residues in contact with ALA 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ILE* 4.0 7.9 - - - +
88B GLU* 3.5 35.0 - - + -
89B CYS* 4.0 17.2 - - - -
92B HIS* 5.9 0.7 - - - -
302B GLY 3.1 19.7 + - - +
303B GLN 3.7 1.3 - - - +
305B ALA* 1.3 75.3 - - - +
307B LYS* 1.3 57.6 + - - +
309B ILE* 3.3 13.0 - - - +
310B TYR* 3.0 27.9 + - - +
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Residues in contact with LYS 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLU* 4.4 22.9 - - + +
303B GLN* 3.1 28.8 + - - +
304B VAL* 3.7 9.9 - - + +
306B ALA* 1.3 75.1 - - - +
308B MET* 1.3 64.3 + - + +
310B TYR* 3.5 5.9 + - - +
311B LYS* 3.2 36.4 + - - +
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Residues in contact with MET 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B MET* 3.9 25.8 - - + -
156B PRO* 4.2 10.5 - - + -
157B SER 3.7 20.9 - - - +
158B ILE* 4.1 14.6 - - - -
304B VAL* 2.7 42.9 + - + +
305B ALA 3.5 4.3 - - - +
307B LYS* 1.3 72.3 - - - +
309B ILE* 1.3 59.0 + - - +
311B LYS* 3.4 6.2 + - - +
312B LEU* 3.0 32.3 + - + +
318B VAL* 3.8 34.0 - - + +
319B THR 4.3 3.8 - - - +
321B ILE* 4.0 15.3 - - + -
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Residues in contact with ILE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 4.0 22.4 - - + -
89B CYS* 4.3 4.9 - - - -
94B LEU* 5.9 0.4 - - + -
122B ALA* 3.6 30.5 - - + -
123B ILE 4.1 10.1 - - - +
124B ILE* 4.1 17.5 - - + -
142B PRO 4.7 2.5 - - - +
144B MET* 3.6 30.7 - - + +
305B ALA 2.7 19.8 + - - +
306B ALA* 3.3 20.6 - - - +
308B MET* 1.3 72.9 - - - +
310B TYR* 1.3 58.2 + - - +
312B LEU* 3.4 16.8 + - + +
313B ILE* 2.9 34.2 + - + +
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Residues in contact with TYR 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B CYS* 6.5 0.2 - - - -
92B HIS* 3.3 63.4 - + + +
94B LEU* 4.1 17.9 - - + -
306B ALA 3.0 18.5 + - - +
307B LYS* 3.9 6.3 - - - +
308B MET 3.3 0.4 - - - -
309B ILE* 1.3 78.9 - - + +
311B LYS* 1.3 58.0 + - + +
313B ILE* 3.2 16.4 + - + +
314B LYS* 3.0 69.8 + - + +
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Residues in contact with LYS 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B LYS* 3.2 20.9 + - - +
308B MET* 3.7 8.1 - - - +
310B TYR* 1.3 78.0 - - + +
312B LEU* 1.3 56.8 + - - +
314B LYS* 3.3 19.0 + - - +
315B GLY 3.0 7.4 + - - -
316B LYS* 2.8 43.1 + - + +
317B ASP 4.7 6.7 + - - +
318B VAL* 3.7 18.8 - - + -
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B PRO* 3.9 25.1 - - + +
143B ILE 4.0 11.4 - - - +
144B MET* 3.9 21.1 - - + -
156B PRO* 4.0 21.3 - - + -
308B MET 3.0 23.4 + - - +
309B ILE* 3.6 25.1 - - + +
310B TYR 3.3 0.4 - - - -
311B LYS* 1.3 72.1 - - - +
313B ILE* 1.3 60.7 + - - +
315B GLY* 2.9 20.5 + - - +
316B LYS 4.4 7.4 - - - +
318B VAL* 3.9 20.6 - - + +
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Residues in contact with ILE 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 4.2 6.1 - - + -
94B LEU* 3.8 28.9 - - + -
121B SER* 3.5 34.1 - - - +
122B ALA* 4.0 17.9 - - + -
142B PRO* 4.1 7.9 - - + +
309B ILE 2.9 23.0 + - - +
310B TYR* 3.5 19.3 - - + +
312B LEU* 1.3 74.9 - - - +
314B LYS* 1.3 61.3 + - + +
315B GLY 3.6 0.7 + - - -
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Residues in contact with LYS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B TYR* 3.0 62.6 + - + +
311B LYS* 3.3 19.5 + - - +
312B LEU 3.1 0.2 - - - -
313B ILE* 1.3 78.8 - - + +
315B GLY* 1.3 59.9 + - - +
316B LYS* 3.3 22.9 + - + -
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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
------------------------------------------------------------
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