Contacts of the helix formed by residues 294 - 310 (chain A) in PDB entry 1QP4
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 LYS 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A TYR* 4.6 20.9 - - + +
76A GLU* 3.1 39.1 + - + +
77A ILE* 4.2 29.6 - - + +
80A ALA* 4.7 3.5 - - - +
275A ASP* 2.9 28.3 - - - -
276A ASN* 2.8 19.9 + - - +
277A VAL* 4.5 2.5 - - + +
278A ARG* 4.5 1.0 - - - +
291A HIS* 4.4 9.3 + - - -
292A GLN* 2.8 30.4 + - + +
293A PRO* 1.3 73.1 - - - +
295A ASP* 1.3 62.9 + - - +
297A LEU* 2.9 8.5 - - - +
298A GLY* 2.7 31.9 + - - -
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Residues in contact with ASP 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA* 4.1 19.1 - - + +
84A ASN* 5.1 0.2 + - - -
278A ARG* 5.0 9.0 + - - -
291A HIS* 5.2 5.7 + - - -
293A PRO* 4.4 2.8 - - - +
294A LYS* 1.3 81.2 + - - +
296A SER* 1.3 70.0 + - - +
298A GLY* 3.0 0.7 + - - -
299A GLU* 2.8 33.1 + - - +
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Residues in contact with SER 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A PRO* 3.1 31.0 + - - +
295A ASP* 1.3 76.8 + - - +
297A LEU* 1.3 59.3 + - - +
299A GLU* 4.4 14.6 - - - -
300A THR* 2.7 41.4 + - - -
321A VAL* 4.4 10.5 - - - -
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Residues in contact with LEU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR* 4.8 3.1 - - - +
77A ILE* 4.3 17.7 - - + -
145A MET* 3.4 46.4 - - + +
158A VAL* 4.2 21.6 - - + +
160A ASP* 4.9 11.0 - - + +
292A GLN* 4.1 23.3 - - + +
293A PRO* 2.9 21.7 + - - +
294A LYS* 2.9 11.2 + - - +
296A SER* 1.3 82.7 - - - +
298A GLY* 1.3 62.7 + - - +
300A THR* 4.4 0.9 - - - -
301A ALA* 3.4 13.0 + - - +
321A VAL* 4.9 9.4 - - + +
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Residues in contact with GLY 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 4.9 2.2 - - - -
80A ALA* 4.4 7.6 - - - -
81A VAL* 4.1 25.6 - - - +
84A ASN* 4.7 1.6 - - - -
145A MET* 4.4 6.3 - - - -
294A LYS 2.7 16.3 + - - -
295A ASP 3.0 3.0 + - - -
297A LEU* 1.3 73.2 - - - +
299A GLU* 1.3 65.9 + - - +
301A ALA* 2.8 16.3 + - - +
302A PHE* 3.0 12.1 + - - +
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Residues in contact with GLU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA* 5.0 0.2 - - - +
84A ASN* 3.6 34.8 - - - +
295A ASP 2.8 17.4 + - - +
296A SER* 4.4 9.4 - - - -
298A GLY* 1.3 71.0 - - - -
300A THR* 1.3 74.0 + - - +
302A PHE* 3.1 2.8 + - - +
303A ASN* 2.8 42.5 + - - +
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Residues in contact with THR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A VAL* 4.6 15.7 - - + -
296A SER* 2.7 28.8 + - - -
297A LEU* 4.4 2.0 - - - -
299A GLU* 1.3 86.3 + - - +
301A ALA* 1.3 62.6 + - - +
303A ASN* 3.3 7.2 + - - +
304A MET* 3.1 22.4 + - - +
319A ILE* 4.0 39.5 - - + +
321A VAL* 6.1 3.3 - - + +
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Residues in contact with ALA 301 (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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81A VAL* 5.8 0.2 - - + -
120A LEU* 4.8 6.3 - - + -
143A VAL* 3.7 22.8 - - + +
145A MET* 4.1 30.7 - - + -
158A VAL* 4.2 7.4 - - + +
297A LEU 3.4 12.4 + - - +
298A GLY 2.8 16.1 + - - +
300A THR* 1.3 73.1 - - - +
302A PHE* 1.3 65.4 + - - +
304A MET* 3.1 5.1 + - - -
305A LEU* 3.0 21.7 + - - +
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Residues in contact with PHE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 4.6 13.9 - - + -
81A VAL* 5.1 3.8 - - + +
84A ASN* 3.1 38.6 - - + -
85A CYS* 3.4 42.6 - - - -
88A LYS* 3.5 21.1 - - + -
90A TYR* 4.4 6.5 - - + -
120A LEU* 4.7 16.9 - - + +
298A GLY 3.0 9.8 + - - +
299A GLU 3.3 9.0 - - - +
301A ALA* 1.3 76.1 - - - +
303A ASN* 1.3 70.9 + - - +
305A LEU* 3.1 12.3 + - + +
306A LEU* 2.9 50.7 + - + +
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Residues in contact with ASN 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASN* 4.8 3.1 + - - +
88A LYS* 4.9 10.7 + - - -
299A GLU* 2.8 39.3 + - - +
300A THR* 3.7 7.3 + - - +
301A ALA 3.1 0.4 - - - -
302A PHE* 1.3 91.6 - - - +
304A MET* 1.3 66.2 + - - +
306A LEU* 3.4 8.6 + - - +
307A ASP* 3.0 21.7 + - - +
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Residues in contact with MET 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A VAL* 4.8 6.5 - - + -
156A ASP* 3.3 45.3 - - + +
157A ALA 3.5 18.6 - - - +
158A VAL* 4.8 3.8 - - - -
300A THR* 3.1 17.5 + - - +
301A ALA* 3.1 7.3 + - - +
303A ASN* 1.3 74.9 - - - +
305A LEU* 1.3 67.8 + - - +
307A ASP* 3.0 7.1 + - - +
308A ARG* 3.0 17.8 + - - +
313A ARG* 3.4 8.6 + - - +
317A GLN* 3.3 18.8 - - + +
318A SER* 3.3 33.4 - - - +
319A ILE* 3.4 33.4 - - + +
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Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 3.9 28.7 - - + -
118A GLY* 4.0 7.0 - - - -
119A LEU 3.9 8.5 - - - +
120A LEU* 3.3 25.1 - - + -
141A PRO* 3.3 39.5 - - + +
142A MET* 3.8 3.6 - - - +
143A VAL* 3.8 18.0 - - + +
156A ASP* 5.5 0.2 - - - -
301A ALA 3.0 11.7 + - - +
302A PHE* 3.2 13.5 - - + +
304A MET* 1.3 78.1 - - - +
306A LEU* 1.3 64.6 + - + +
308A ARG* 3.0 7.2 + - + +
309A ILE* 2.8 32.5 + - + +
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Residues in contact with LEU 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 5.7 0.2 - - + -
88A LYS* 4.1 31.6 - - + +
90A TYR* 4.0 32.8 - - + +
302A PHE* 2.9 38.1 + - + +
303A ASN* 3.6 12.1 - - - +
305A LEU* 1.3 75.9 - - + +
307A ASP* 1.3 55.2 + - - +
309A ILE* 4.0 12.1 - - + -
310A VAL* 2.6 51.5 + - + +
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Residues in contact with ASP 307 (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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303A ASN 3.0 10.6 + - - +
304A MET* 3.1 12.3 - - - +
306A LEU* 1.3 75.7 - - - +
308A ARG* 1.3 62.6 + - - +
310A VAL* 4.9 0.7 - - - -
311A ASN* 2.7 71.9 + - - +
312A LYS 3.4 0.3 + - - -
313A ARG* 2.7 37.1 + - - +
317A GLN* 4.1 6.5 + - - +
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Residues in contact with ARG 308 (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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138A ARG 5.2 5.3 + - - -
141A PRO* 4.5 23.3 - - + +
142A MET 4.7 13.6 - - - +
153A ASP 4.6 0.8 + - - -
154A PHE 3.8 16.8 + - - -
155A THR* 3.8 12.4 - - - +
156A ASP* 3.1 23.0 + - - +
304A MET 3.0 3.9 + - - +
305A LEU* 3.0 10.4 + - - +
307A ASP* 1.3 77.1 - - - +
309A ILE* 1.3 59.1 + - - +
312A LYS* 2.8 34.5 + - - +
313A ARG* 3.3 46.8 + - - +
314A GLU* 3.8 17.0 + - - +
315A GLU 4.4 0.2 + - - -
316A PRO* 3.1 39.2 - - - +
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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
----------------------------------------------------------
62A ILE* 4.9 1.8 - - + -
90A TYR* 4.0 21.3 - - + +
117A ASP* 3.9 35.2 - - + +
118A GLY* 4.3 4.7 - - - +
141A PRO* 4.1 12.8 - - + +
305A LEU* 2.8 41.0 + - + +
306A LEU* 3.3 19.1 - - + +
308A ARG* 1.3 80.9 - - - +
310A VAL* 1.3 71.2 + - + +
312A LYS* 3.6 10.6 + - - +
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Residues in contact with VAL 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A TYR* 5.6 1.6 - - - +
306A LEU* 2.6 44.1 + - + +
307A ASP* 4.9 0.2 - - - -
309A ILE* 1.3 78.3 - - + +
311A ASN* 1.3 72.9 + - - +
312A LYS* 2.7 22.0 + - - +
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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