Contacts of the helix formed by residues 288 - 309 (chain A) in PDB entry 1KOJ
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 GLY 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A CYS* 6.1 0.4 - - - -
136A ARG* 3.5 23.7 - - - +
284A ALA* 2.8 20.1 + - - +
287A VAL* 1.3 84.4 - - - +
289A PHE* 1.3 65.2 + - - -
290A ASP 3.4 3.1 - - - -
291A ASN 3.6 0.2 + - - -
292A PHE* 3.3 19.2 + - - +
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Residues in contact with PHE 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 5.8 0.2 - - - -
125A LEU* 3.2 37.2 - - + -
126A ASP* 5.7 0.4 - - - -
128A MET* 3.8 11.7 - - + -
129A LYS* 3.4 63.7 - - + -
132A CYS* 4.6 8.0 - - + +
284A ALA* 3.8 19.6 + - + -
288A GLY* 1.3 69.7 - - - -
290A ASP* 1.3 60.9 + - - +
292A PHE* 3.5 25.0 - + - +
293A GLU* 2.9 63.6 + - + +
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Residues in contact with ASP 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A LYS* 4.3 14.6 + - - -
288A GLY* 3.4 1.2 - - - -
289A PHE* 1.3 77.4 - - - +
291A ASN* 1.3 60.4 + - - +
293A GLU* 3.2 17.8 + - - +
294A GLN* 3.0 32.8 + - + +
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Residues in contact with ASN 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170A LEU* 6.0 0.7 - - - -
173A TYR* 3.6 30.7 + - - +
287A VAL* 2.7 42.2 + - + +
288A GLY 3.6 1.0 + - - -
289A PHE 3.3 0.2 - - - -
290A ASP* 1.3 79.0 - - - +
292A PHE* 1.3 58.0 + - - +
294A GLN* 3.0 13.3 + - - +
295A LEU* 2.9 24.9 + - - +
483A PRO* 3.5 28.0 - - + +
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Residues in contact with PHE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A LEU* 4.2 9.2 - - + -
128A MET* 4.1 15.3 - - + -
275A LEU 3.8 22.4 - - - -
276A TRP 4.1 7.0 - - - -
277A SER 4.0 13.0 - - - -
280A GLY* 3.7 17.9 - - - -
283A ILE* 3.7 24.2 - - + -
284A ALA* 4.1 11.0 - - + -
287A VAL* 4.4 3.7 - - + +
288A GLY 3.3 13.2 + - - +
289A PHE* 3.5 31.6 - + - +
290A ASP 3.3 0.2 - - - -
291A ASN* 1.3 78.2 - - - +
293A GLU* 1.3 58.2 + - - +
295A LEU* 3.2 19.9 + - + +
296A LEU* 3.0 52.7 + - + +
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Residues in contact with GLU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 3.2 35.7 + - - +
129A LYS* 4.7 8.2 + - - +
289A PHE* 2.9 55.3 + - + +
290A ASP* 3.5 18.1 - - - +
291A ASN 3.2 0.2 - - - -
292A PHE* 1.3 74.0 - - - +
294A GLN* 1.3 62.8 + - - +
296A LEU* 3.3 11.6 + - + +
297A SER* 2.8 30.9 + - - -
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Residues in contact with GLN 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A HIS* 4.9 14.9 + - - +
290A ASP* 3.0 20.5 + - + +
291A ASN* 3.0 17.5 + - - +
293A GLU* 1.3 77.1 - - - +
295A LEU* 1.3 59.2 + - - +
297A SER* 3.3 9.4 + - - -
298A GLY 2.9 24.8 + - - -
483A PRO* 3.9 13.7 - - + -
484A PHE* 3.2 32.1 - - - +
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Residues in contact with LEU 295 (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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166A VAL* 4.2 17.0 - - + -
170A LEU* 5.0 3.4 - - + -
275A LEU* 4.1 21.3 - - + -
276A TRP* 3.7 15.6 - - + -
283A ILE* 4.4 4.0 - - + -
291A ASN 2.9 11.9 + - - +
292A PHE* 3.3 32.3 - - + +
294A GLN* 1.3 77.3 - - - +
296A LEU* 1.3 62.4 + - + +
298A GLY 3.2 8.5 + - - -
299A ALA 3.2 10.0 + - - -
483A PRO* 3.4 19.7 + - + +
486A LEU* 4.3 17.5 - - + -
487A GLY* 3.5 34.7 - - - +
490A ILE* 4.7 3.8 - - + -
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Residues in contact with LEU 296 (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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102A LEU 4.4 7.4 - - - +
103A ARG* 3.5 21.0 - - + +
105A ARG* 3.7 29.2 - - - +
125A LEU* 4.1 14.6 - - + -
276A TRP* 3.6 48.5 - - + +
292A PHE* 3.0 43.0 + - + +
293A GLU* 3.6 10.5 - - + +
295A LEU* 1.3 73.6 - - + +
297A SER* 1.3 60.9 + - - +
299A ALA 3.2 1.7 + - - -
300A HIS* 2.9 29.0 + - - +
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Residues in contact with SER 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A HIS* 5.0 2.4 + - - -
105A ARG* 4.1 12.5 - - - +
293A GLU 2.8 17.1 + - - -
294A GLN* 3.5 14.3 + - - -
296A LEU* 1.3 77.9 - - - +
298A GLY* 1.3 62.8 + - - +
300A HIS* 3.2 9.5 + - - +
301A TRP* 3.0 19.4 + - - +
484A PHE* 3.0 24.7 - - - -
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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
----------------------------------------------------------
294A GLN 2.9 11.1 + - - -
295A LEU 3.2 2.0 + - - -
296A LEU 3.2 0.2 - - - -
297A SER* 1.3 77.7 + - - +
299A ALA* 1.3 60.9 + - - +
301A TRP* 3.3 11.3 + - - +
302A MET 3.3 8.7 + - - -
484A PHE* 3.1 39.0 - - - -
488A ALA* 3.4 18.4 - - - +
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Residues in contact with ALA 299 (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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103A ARG* 3.7 20.9 - - - +
276A TRP* 3.5 32.1 - - + -
295A LEU 3.2 4.6 + - - -
296A LEU 3.2 7.0 + - - +
298A GLY* 1.3 75.2 - - - +
300A HIS* 1.3 58.3 + - - +
302A MET* 3.2 3.6 + - - +
303A ASP* 2.9 33.8 + - - +
487A GLY 3.4 14.4 - - - +
491A ALA* 3.7 7.8 - - + +
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Residues in contact with HIS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A VAL 5.3 0.4 + - - -
103A ARG* 3.2 23.5 + - - +
104A ASN* 3.5 28.9 - - + -
105A ARG* 3.9 14.6 - - + -
106A SER* 2.7 30.8 + - - -
296A LEU 2.9 9.4 + - - +
297A SER* 3.4 13.2 - - - +
299A ALA* 1.3 77.8 - - - +
301A TRP* 1.3 60.8 + - - +
303A ASP* 3.3 14.3 + - + +
304A GLN* 3.1 46.0 + - + +
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Residues in contact with TRP 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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43A LEU* 3.6 31.2 - - + -
44A ASN 3.6 19.7 + - - -
45A THR* 3.7 42.4 + - + +
46A ASN* 5.6 1.8 + - - -
297A SER 3.0 12.6 + - - +
298A GLY 3.6 8.1 - - - +
299A ALA 3.2 0.2 - - - -
300A HIS* 1.3 77.2 - - - +
302A MET* 1.3 94.0 + - + +
304A GLN* 3.1 15.1 + - + +
305A HIS* 2.9 37.1 + - + -
484A PHE* 3.9 14.8 - + + -
488A ALA* 4.9 3.8 - - + -
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Residues in contact with MET 302 (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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43A LEU* 4.1 13.2 - - + -
50A ILE* 4.5 6.5 - - + -
298A GLY 3.3 5.9 + - - +
299A ALA 3.2 8.1 + - - +
301A TRP* 1.3 105.8 - - + +
303A ASP* 1.3 58.1 + - - +
305A HIS* 3.2 23.6 + - - +
306A PHE* 2.9 28.8 + - - +
315A ALA* 4.7 0.4 - - - -
316A PRO* 4.3 4.9 - - - -
488A ALA* 3.5 35.2 - - + +
491A ALA* 3.8 9.0 - - + +
492A MET* 3.5 40.8 - - + +
495A HIS* 4.7 3.8 - - + -
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Residues in contact with ASP 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 3.8 18.0 - - + -
100A VAL* 3.8 15.0 - - - +
103A ARG* 2.8 42.5 + - - +
299A ALA 2.9 17.2 + - - +
300A HIS* 3.5 14.8 + - + +
301A TRP 3.2 0.4 - - - -
302A MET* 1.3 76.6 - - - +
304A GLN* 1.3 57.4 + - + +
306A PHE* 3.3 4.0 + - - +
307A ARG* 2.9 29.3 + - - +
491A ALA* 4.2 1.0 - - - +
495A HIS* 2.5 35.0 + - - -
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Residues in contact with GLN 304 (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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106A SER* 4.5 8.0 + - - -
300A HIS* 3.1 43.6 + - + +
301A TRP* 3.1 13.9 + - + +
303A ASP* 1.3 76.8 - - + +
305A HIS* 1.3 61.2 + - - +
307A ARG* 4.4 5.8 - - - +
308A THR* 2.8 44.9 + - + +
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Residues in contact with HIS 305 (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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43A LEU* 3.5 30.3 - - + +
301A TRP* 2.9 36.5 + + + +
302A MET* 3.4 19.3 - - - +
304A GLN* 1.3 75.8 - - - +
306A PHE* 1.3 65.7 + - - +
308A THR* 4.4 1.6 - - - -
309A THR* 2.7 54.7 + - + -
313A LYS 3.6 14.8 + - - -
314A ASN* 3.9 1.8 - - - -
315A ALA* 3.0 27.0 + - + +
316A PRO* 3.7 20.0 - - + -
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Residues in contact with PHE 306 (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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76A VAL* 5.0 3.6 - - + -
80A ARG* 3.1 46.4 + - + -
83A MET* 5.8 0.4 - - - -
84A PHE* 4.0 10.8 - + - -
302A MET 2.9 16.5 + - - +
303A ASP 3.5 3.4 - - - +
305A HIS* 1.3 78.9 - - - +
307A ARG* 1.3 55.2 + - - +
314A ASN* 2.9 38.0 + - - +
316A PRO* 4.0 12.6 - - + -
317A VAL* 3.9 10.5 - - + -
495A HIS* 3.4 45.3 - + + -
498A PHE* 3.7 27.4 - + - -
499A VAL* 3.8 23.1 - - + -
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Residues in contact with ARG 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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80A ARG* 3.4 34.1 + - - +
81A GLU* 2.6 41.4 + - - +
84A PHE* 3.5 45.8 + - + +
85A ASN* 3.5 19.0 + - - -
108A THR* 6.2 1.8 - - - +
303A ASP 2.9 17.3 + - - +
304A GLN* 3.9 6.7 - - - +
305A HIS 3.2 0.2 - - - -
306A PHE* 1.3 78.0 - - - +
308A THR* 1.3 66.8 + - + +
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Residues in contact with THR 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304A GLN* 2.8 30.2 + - + +
305A HIS* 4.2 1.7 + - - -
307A ARG* 1.3 88.5 - - + +
309A THR* 1.3 65.3 + - - +
310A PRO* 3.8 6.1 - - - +
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Residues in contact with THR 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLU* 5.8 0.2 - - - +
80A ARG* 4.8 3.5 + - - -
305A HIS* 2.7 44.0 + - + -
306A PHE 4.6 0.7 - - - +
307A ARG 3.7 1.0 - - - -
308A THR* 1.3 80.3 + - - +
310A PRO* 1.3 77.0 - - + +
311A LEU* 3.3 3.5 + - - +
313A LYS* 3.1 40.6 - - + +
314A ASN* 3.0 21.7 + - - +
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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