Contacts of the helix formed by residues 286 - 305 (chain A) in PDB entry 4KZK
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 ASN 286 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TRP* 3.8 2.9 - - - -
285A LEU* 1.3 76.7 - - - +
287A PRO* 1.4 60.2 - - - +
288A ARG* 3.0 25.0 + - - +
289A LEU* 3.1 52.8 + - + +
290A HIS* 3.5 13.8 + - + -
314A THR* 5.6 2.0 + - - -
315A SER 4.6 9.4 + - - +
331A LEU* 4.3 31.8 + - + +
333A LEU* 4.0 5.8 - - - +
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Residues in contact with PRO 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A TRP* 3.6 27.8 - - + -
49A ASP* 3.6 41.5 - - + +
50A GLU* 4.2 3.9 - - - +
52A ARG* 5.5 0.2 - - - +
53A PHE* 3.8 20.5 - - + +
285A LEU 3.3 11.0 - - - +
286A ASN* 1.4 81.0 - - - +
288A ARG* 1.3 60.5 + - - +
290A HIS* 3.8 4.0 - - + +
291A GLY* 2.8 27.9 + - - -
333A LEU* 3.8 18.6 - - + -
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Residues in contact with ARG 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 3.3 31.6 - - + -
56A GLN* 2.7 33.5 + - - +
286A ASN* 3.0 15.7 + - - +
287A PRO* 1.3 80.9 - - - +
289A LEU* 1.3 61.2 + - + +
292A TYR* 2.8 48.1 + - + +
293A ASP* 3.1 10.9 + - - +
331A LEU 4.0 11.7 + - - -
332A GLY* 3.0 32.5 + - - -
333A LEU* 4.9 1.3 - - + -
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A MET* 3.2 23.9 - - + +
286A ASN* 3.1 37.5 + - + +
288A ARG* 1.3 82.0 - - + +
290A HIS* 1.3 65.1 + - + +
293A ASP* 3.3 43.0 + - - +
294A THR 3.3 2.4 + - - -
314A THR* 3.7 26.0 - - + -
315A SER 5.5 2.0 - - - +
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Residues in contact with HIS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.6 11.8 - - - -
46A TRP* 3.6 17.7 - + + -
50A GLU* 3.4 18.6 - - + +
118A VAL* 3.6 9.5 - - + +
119A ASP* 2.8 26.5 + - - -
136A MET* 3.7 17.4 - - - +
137A GLY* 3.7 28.2 + - - -
138A ILE* 3.8 5.5 - - + +
285A LEU* 5.9 0.2 - - - +
286A ASN 3.5 14.1 + - - +
287A PRO 4.2 2.2 - - - +
288A ARG 3.4 0.2 - - - -
289A LEU* 1.3 75.1 - - - +
291A GLY* 1.3 52.1 + - - +
294A THR* 2.7 24.3 + - - +
314A THR* 2.8 33.6 + - + +
600A GAL 3.7 7.9 - - - -
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Residues in contact with GLY 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 4.0 4.7 - - - -
50A GLU* 3.4 24.0 - - - +
53A PHE* 4.3 0.2 - - - -
54A ALA* 3.4 11.7 - - - +
287A PRO 2.8 19.5 + - - -
290A HIS* 1.3 75.3 - - - +
292A TYR* 1.3 58.6 + - - +
294A THR* 3.4 4.1 + - - -
295A SER* 2.7 28.2 + - - -
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Residues in contact with TYR 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A PHE* 3.3 17.0 - - + +
56A GLN* 3.6 20.4 - - + -
57A ALA* 3.3 36.3 - - - +
60A ASP* 2.7 36.3 + - - +
61A LYS* 5.3 3.0 - - + +
288A ARG* 2.8 38.4 + - + +
291A GLY* 1.3 70.8 - - - -
293A ASP* 1.3 68.5 + - - -
295A SER* 3.1 4.5 + - - -
296A VAL* 3.0 49.3 + - + +
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Residues in contact with ASP 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A MET* 4.2 9.1 - - + +
288A ARG* 3.1 8.8 + - - +
289A LEU* 3.3 41.2 + - - +
292A TYR* 1.3 86.7 - - - +
294A THR* 1.3 60.5 + - - +
296A VAL* 3.4 5.8 + - - +
297A ASN* 2.9 39.5 + - - +
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Residues in contact with THR 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A PHE* 3.8 7.6 - - - -
92A ILE* 3.7 9.4 - - - -
116A MET* 3.6 22.6 - - - +
117A SER 5.2 0.4 - - - +
118A VAL* 4.2 9.4 - - + -
136A MET* 3.7 38.6 - - + -
289A LEU 3.3 1.0 + - - +
290A HIS* 2.7 28.8 + - - +
291A GLY* 3.4 7.6 + - - -
293A ASP* 1.3 75.8 - - - +
295A SER* 1.3 63.4 + - - +
297A ASN* 3.2 7.0 + - - +
298A MET* 2.9 29.8 + - - +
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.9 5.6 - - - +
37A PHE* 3.9 11.1 - - - -
54A ALA* 3.4 14.9 - - - +
57A ALA* 3.7 17.3 - - - -
63A PHE* 3.9 14.9 - - - -
65A LEU* 4.8 1.9 - - - +
92A ILE* 3.7 10.6 - - - +
291A GLY 2.7 22.4 + - - -
292A TYR 3.1 5.2 + - - -
294A THR* 1.3 80.7 + - - +
296A VAL* 1.3 58.2 + - - +
298A MET* 3.4 2.3 + - - +
299A TYR* 2.8 28.6 + - - +
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Residues in contact with VAL 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A ALA* 4.3 5.2 - - + -
61A LYS* 4.0 33.9 - - + +
292A TYR* 3.0 43.6 + - + +
293A ASP* 3.9 6.1 - - - +
295A SER* 1.3 75.0 - - - +
297A ASN* 1.3 63.9 + - - +
299A TYR* 3.5 5.4 - - - +
300A ASP* 2.8 47.2 + - - +
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Residues in contact with ASN 297 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A MET* 3.9 17.5 - - + +
136A MET* 4.5 11.7 - - - +
293A ASP* 2.9 26.5 + - - +
294A THR* 3.5 7.9 - - - +
296A VAL* 1.3 79.0 - - - +
298A MET* 1.3 57.5 + - - +
300A ASP* 3.9 5.5 - - - +
301A TRP* 3.0 28.6 + - - +
306A ARG 5.0 1.0 - - - +
308A PRO* 4.8 4.5 - - + +
309A PRO* 3.8 35.0 - - + +
312A VAL* 5.5 1.6 - - - +
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Residues in contact with MET 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.7 27.6 - - + -
90A GLY* 4.0 4.3 - - - -
91A VAL 3.6 19.7 - - - +
92A ILE* 4.0 9.0 - - + -
114A LYS* 3.5 41.7 - - - +
116A MET* 3.6 28.1 - - + +
294A THR 2.9 16.1 + - - +
295A SER 3.6 4.7 - - - +
297A ASN* 1.3 74.1 - - - +
299A TYR* 1.3 66.4 + - - +
301A TRP* 3.1 15.7 + - + +
302A ILE* 2.9 35.1 + - + +
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Residues in contact with TYR 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 4.0 24.5 - - + +
35A ILE* 3.8 8.7 - - + +
61A LYS* 3.3 48.4 + - + -
62A HIS* 4.7 2.7 + - - +
63A PHE* 3.6 26.0 - + + -
295A SER 2.8 20.6 + - - +
296A VAL* 3.5 8.3 - - - +
298A MET* 1.3 72.3 - - - +
300A ASP* 1.3 72.2 + - - +
302A ILE* 3.2 4.7 + - - +
303A THR* 2.8 61.9 + - + +
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Residues in contact with ASP 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LYS* 3.9 11.6 + - - -
296A VAL* 2.8 34.6 + - - +
297A ASN* 3.9 6.4 - - - +
299A TYR* 1.3 91.3 - - - +
301A TRP* 1.3 58.2 + - - +
303A THR* 3.7 5.3 + - - -
304A GLN* 2.9 29.6 + - + +
305A ASN 3.3 5.0 + - - -
306A ARG* 3.4 46.6 + - + +
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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
----------------------------------------------------------
114A LYS* 3.6 48.1 - - + +
115A LEU 3.5 36.6 - - - -
116A MET* 4.4 5.4 - - + -
132A ASP 4.8 5.2 - - - -
134A PRO* 3.6 23.1 - - + -
297A ASN 3.0 17.9 + - - +
298A MET* 3.1 17.9 + - + +
300A ASP* 1.3 77.2 - - - +
302A ILE* 1.3 61.1 + - - +
305A ASN* 3.1 34.5 + - - +
306A ARG 3.4 24.2 + - - +
307A THR* 5.0 0.6 - - - +
308A PRO* 3.8 23.7 - - + +
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Residues in contact with ILE 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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33A VAL* 4.4 14.1 - - + -
35A ILE* 3.8 21.1 - - + -
89A GLN* 3.9 49.6 - - + +
114A LYS* 4.1 16.1 + - + +
298A MET* 2.9 41.4 + - + +
299A TYR* 3.6 6.1 - - - +
301A TRP* 1.3 78.6 - - - +
303A THR* 1.3 71.1 + - + +
305A ASN* 4.4 1.4 + - - -
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Residues in contact with THR 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A VAL* 3.9 19.3 - - + -
299A TYR* 2.8 68.2 + - + +
300A ASP* 3.7 5.0 + - - -
302A ILE* 1.3 78.4 - - + +
304A GLN* 1.3 63.0 + - - +
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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
----------------------------------------------------------
300A ASP* 2.9 16.0 + - + +
303A THR* 1.3 79.5 + - - +
305A ASN* 1.3 71.8 + - - +
306A ARG* 3.1 15.6 + - + +
----------------------------------------------------------
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Residues in contact with ASN 305 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LYS* 4.7 5.9 - - - -
301A TRP* 3.1 33.6 + - - +
302A ILE 4.4 1.4 + - - +
303A THR 3.7 1.2 - - - -
304A GLN* 1.3 79.3 - - - +
306A ARG* 1.3 62.1 + - - +
307A THR* 3.5 4.5 + - - -
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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) + - + + + + + -
------------------------------------------------------------
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