Contacts of the helix formed by residues 297 - 314 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A VAL* 3.8 15.9 - - + -
295A SER 4.2 0.4 - - - +
296A GLN* 1.3 82.0 - - + +
298A VAL* 1.3 52.7 - - - +
299A LYS* 3.4 3.1 + - - -
300A GLU* 3.6 19.4 + - + +
301A MET* 2.8 37.5 + - + +
323A LEU* 3.9 24.0 - - + -
324A SER 3.3 28.3 - - - +
325A THR* 4.5 0.7 - - - -
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Residues in contact with VAL 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.8 33.7 - - + +
80A GLU* 4.1 36.6 - - + +
81A VAL* 4.0 17.4 - - + +
84A GLU* 4.0 7.3 - - + +
280A ASP* 5.2 5.4 - - + +
296A GLN* 2.9 21.2 + - + +
297A PRO* 1.3 72.0 - - - +
299A LYS* 1.3 65.6 + - + +
301A MET* 3.8 6.1 - - - +
302A GLY* 2.9 27.7 + - - -
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Residues in contact with LYS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 3.7 35.4 - - + +
297A PRO 3.4 0.4 - - - -
298A VAL* 1.3 83.2 - - + +
300A GLU* 1.3 65.6 + - - +
302A GLY* 3.9 0.5 - - - -
303A GLN* 3.0 26.7 + - - +
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Residues in contact with GLU 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A PRO* 3.6 18.4 + - + +
299A LYS* 1.3 78.3 - - - +
301A MET* 1.3 63.8 + - - +
303A GLN* 4.7 3.6 - - - -
304A VAL* 2.8 45.6 + - + +
323A LEU* 3.4 32.4 - - + +
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Residues in contact with MET 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 3.8 36.8 - - + -
81A VAL* 4.4 5.4 - - + -
146A LEU* 4.1 29.4 - - + -
147A ASP* 4.8 7.2 - - - +
158A ILE* 3.5 23.9 - - + +
159A THR* 5.4 1.8 - - - -
160A VAL* 4.0 27.1 - - + -
296A GLN* 4.2 0.4 - - - +
297A PRO* 2.8 30.6 + - + +
298A VAL* 3.8 5.2 - - - +
300A GLU* 1.3 72.6 - - - +
302A GLY* 1.3 56.7 + - - +
305A ALA* 2.9 33.3 + - - +
323A LEU* 3.8 13.6 - - + +
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Residues in contact with GLY 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A VAL* 4.0 6.3 - - - +
84A GLU* 3.9 10.8 - - - -
85A ILE* 3.5 30.7 - - - +
298A VAL 2.9 19.9 + - - -
301A MET* 1.3 70.3 - - - +
303A GLN* 1.3 59.7 + - - +
305A ALA 3.5 0.2 + - - -
306A ALA* 2.9 31.0 + - - +
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Residues in contact with GLN 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A GLU* 4.4 11.6 + - - +
87A HIS* 5.3 6.7 - - - -
88A GLU* 2.8 35.4 + - - +
91A LYS* 4.7 2.6 - - - +
299A LYS 3.0 18.2 + - - +
300A GLU* 3.9 4.0 - - - +
302A GLY* 1.3 75.7 - - - +
304A VAL* 1.3 65.0 + - + +
306A ALA* 3.2 7.9 + - - +
307A LYS* 3.0 54.7 + - - +
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Residues in contact with VAL 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A ILE* 3.9 18.8 - - + -
300A GLU* 2.8 45.3 + - + +
303A GLN* 1.3 75.2 - - + +
305A ALA* 1.3 57.1 + - - +
307A LYS* 3.2 10.8 + - + +
308A MET* 2.9 38.0 + - + +
321A ILE* 4.1 28.9 - - + -
323A LEU* 5.3 2.5 - - + -
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 4.5 7.2 - - + -
124A ILE* 5.1 3.1 - - + -
144A MET* 3.6 28.7 - - + +
146A LEU* 4.0 18.4 - - + -
158A ILE* 4.0 4.6 - - + +
301A MET 2.9 23.0 + - - +
302A GLY 3.9 2.9 - - - +
304A VAL* 1.3 69.4 - - - +
306A ALA* 1.3 62.5 - - - +
308A MET* 3.4 5.9 + - - +
309A ILE* 2.8 33.5 + - - +
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 3.8 9.8 - - - +
88A GLU* 3.5 30.3 - - + -
89A CYS* 3.8 19.5 - - - -
92A HIS* 5.8 0.7 - - - -
302A GLY 2.9 20.0 + - - +
303A GLN 3.5 5.2 - - - +
305A ALA* 1.3 75.1 - - - +
307A LYS* 1.3 62.0 + - - +
309A ILE* 3.4 12.3 - - - +
310A TYR* 3.2 23.6 + - - +
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Residues in contact with LYS 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 3.9 21.1 - - + +
303A GLN* 3.0 47.8 + - + +
304A VAL* 3.6 11.9 - - + +
305A ALA 3.2 0.2 - - - -
306A ALA* 1.3 73.9 - - - +
308A MET* 1.3 64.5 + - - +
310A TYR* 3.2 7.2 + - - +
311A LYS* 3.0 37.5 + - - +
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Residues in contact with MET 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A MET* 4.0 22.2 - - + -
156A PRO* 4.1 14.6 - - + -
157A SER 3.9 18.6 - - - +
158A ILE* 4.0 20.9 - - - -
304A VAL* 2.9 27.1 + - + +
305A ALA* 3.5 5.2 - - - +
307A LYS* 1.3 74.6 - - - +
309A ILE* 1.3 63.1 + - - +
310A TYR 3.2 0.3 + - - -
311A LYS* 3.2 9.2 + - - +
312A LEU* 3.0 21.8 + - + +
318A VAL* 3.6 38.3 - - + +
319A THR 4.1 5.8 - - - +
321A ILE* 4.0 20.4 - - + -
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Residues in contact with ILE 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 4.2 11.2 - - + -
89A CYS* 4.2 15.5 - - - -
122A ALA* 3.5 31.2 - - + -
123A ILE 4.0 10.8 - - - +
124A ILE* 4.1 15.9 - - + -
142A PRO 4.5 3.4 - - - +
144A MET* 3.7 29.6 - - + +
305A ALA 2.8 18.5 + - - +
306A ALA* 3.4 17.9 - - - +
308A MET* 1.3 74.3 - - - +
310A TYR* 1.3 60.4 + - - +
312A LEU* 3.4 17.0 + - + +
313A ILE* 2.9 34.3 + - + +
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Residues in contact with TYR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A CYS* 6.1 1.6 - - - -
92A HIS* 3.5 59.8 + + + +
94A LEU* 4.2 17.7 - - + -
306A ALA 3.2 17.3 + - - +
307A LYS* 3.6 6.1 - - - +
308A MET 3.2 0.6 - - - -
309A ILE* 1.3 77.0 - - + +
311A LYS* 1.3 64.5 + - + +
313A ILE* 3.3 10.3 + - + +
314A LYS* 2.9 69.9 + - + +
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307A LYS* 3.0 24.2 + - - +
308A MET* 3.4 10.6 - - - +
310A TYR* 1.3 79.9 - - + +
312A LEU* 1.3 56.8 + - - +
314A LYS* 3.1 8.5 + - - +
315A GLY 3.0 8.0 + - - -
316A LYS* 2.9 42.2 + - + +
317A ASP 4.4 8.7 - - - +
318A VAL* 3.5 20.0 - - + -
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Residues in contact with LEU 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A PRO* 4.1 21.7 - - + +
143A ILE 4.1 15.0 - - - +
144A MET* 4.2 6.1 - - + -
156A PRO* 4.0 28.0 - - + -
308A MET* 3.0 17.4 + - + +
309A ILE* 3.5 27.1 - - + +
311A LYS* 1.3 72.3 - - - +
313A ILE* 1.3 60.7 + - - +
314A LYS 3.0 1.3 - - - -
315A GLY* 2.8 21.1 + - - +
316A LYS 4.1 9.4 - - - +
318A VAL* 3.8 21.8 - - + +
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Residues in contact with ILE 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ILE* 4.3 9.9 - - + -
94A LEU* 3.6 31.9 - - + -
121A SER* 3.6 37.2 - - - +
122A ALA* 3.9 13.9 - - + -
142A PRO* 4.2 9.7 - - + +
309A ILE 2.9 23.1 + - - +
310A TYR* 3.3 14.1 + - + +
312A LEU* 1.3 75.7 - - - +
314A LYS* 1.3 74.5 + - + +
315A GLY 3.5 0.5 + - - -
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Residues in contact with LYS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A TYR* 2.9 56.5 + - + +
311A LYS* 3.5 10.8 - - - +
312A LEU 3.0 0.4 - - - -
313A ILE* 1.3 89.4 - - + +
315A GLY* 1.3 60.4 + - - +
316A LYS* 3.3 13.6 + - + +
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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
------------------------------------------------------------
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