Contacts of the helix formed by residues 291 - 302 (chain A) in PDB entry 5KFV
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 291 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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287A GLN* 2.9 21.4 + - - -
288A SER 4.7 0.2 - - - -
289A HIS 3.6 1.6 - - - -
290A PHE* 1.3 78.6 - - - +
292A GLU* 1.3 61.3 + - - +
293A LYS 3.4 2.9 - - - -
295A GLY 2.8 26.2 + - - -
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Residues in contact with GLU 292 (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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287A GLN* 3.4 27.1 + - - +
291A GLY* 1.3 71.1 - - - +
293A LYS* 1.3 62.7 + - - +
296A SER* 3.2 28.3 + - - +
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Residues in contact with LYS 293 (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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291A GLY 3.4 0.4 - - - -
292A GLU* 1.3 77.0 - - - +
294A ASN* 1.3 71.5 + - - +
296A SER* 3.4 3.9 + - - -
297A TRP* 2.9 31.5 + - + +
10T G 4.0 43.5 + - - -
11T C 4.7 19.7 + - - +
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Residues in contact with ASN 294 (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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262A LEU* 3.7 35.5 - - + +
290A PHE* 3.1 31.9 + - + +
291A GLY 3.6 1.0 + - - -
293A LYS* 1.3 89.1 + - - +
295A GLY* 1.3 54.0 + - - +
297A TRP* 3.2 10.0 + - + +
298A LEU* 2.7 42.5 + - + +
11T C 5.8 2.1 + - - -
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Residues in contact with GLY 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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283A GLU 4.7 0.9 - - - -
286A LEU* 3.7 18.0 - - - +
287A GLN* 3.7 25.4 - - - -
290A PHE* 4.4 0.4 - - - +
291A GLY 2.8 23.0 + - - -
294A ASN* 1.3 74.1 - - - +
296A SER* 1.3 55.9 + - - +
298A LEU* 3.4 2.6 + - - -
299A TYR* 2.9 30.0 + - - +
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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
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283A GLU* 2.6 30.6 + - - +
287A GLN* 2.9 21.6 + - - +
292A GLU* 3.2 13.0 + - - +
293A LYS* 3.9 3.8 - - - -
295A GLY* 1.3 71.1 - - - +
297A TRP* 1.3 67.3 + - - +
299A TYR* 3.4 1.7 + - - +
300A ALA* 3.2 24.4 + - - +
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Residues in contact with TRP 297 (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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221A VAL* 3.8 23.3 - - + -
255A ILE* 3.7 15.3 - - + -
256A ARG* 3.7 8.3 - - - -
257A SER* 3.4 26.5 - - - -
258A LEU* 4.0 11.0 - - + -
262A LEU* 6.0 1.8 - - + -
293A LYS* 2.9 19.7 + - + +
294A ASN* 3.5 11.2 - - + +
296A SER* 1.3 78.0 - - - +
298A LEU* 1.3 84.9 + - + +
300A ALA* 3.7 3.1 - - - +
301A MET* 2.8 47.7 + - + +
305A ILE 4.7 0.2 - - - +
306A GLU* 3.0 31.9 + - + +
308A ASP* 6.3 0.4 - - + -
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Residues in contact with LEU 298 (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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258A LEU* 3.9 23.3 - - + -
262A LEU* 5.4 3.4 - - + -
266A VAL* 4.2 13.7 - - + -
275A MET* 4.5 1.3 - - + -
278A LEU* 4.1 21.9 - - + +
286A LEU* 4.0 13.9 - - + -
290A PHE* 3.6 36.8 - - + -
294A ASN* 2.7 29.2 + - + +
295A GLY* 3.8 4.3 - - - +
297A TRP* 1.3 99.2 - - + +
299A TYR* 1.3 63.2 + - - +
301A MET* 3.9 2.0 - - - +
302A CYS* 3.0 28.2 + - - +
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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
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281A PHE 3.7 13.0 - - - -
282A THR* 3.9 2.5 - - - -
283A GLU* 3.4 55.9 - - + -
286A LEU* 3.7 10.3 - - + +
295A GLY 2.9 18.3 + - - +
296A SER 3.7 5.4 - - - +
297A TRP 3.3 0.2 - - - -
298A LEU* 1.3 78.4 - - - +
300A ALA* 1.3 65.8 + - + +
302A CYS* 3.4 4.4 - - - -
303A ARG* 2.9 69.4 + - - +
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Residues in contact with ALA 300 (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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296A SER 3.2 13.3 + - - +
297A TRP* 3.9 2.5 - - - +
299A TYR* 1.3 84.9 - - + +
301A MET* 1.3 66.4 + - - +
303A ARG* 3.0 13.3 + - - +
304A GLY 3.3 0.2 + - - -
305A ILE* 2.9 51.8 + - + +
306A GLU* 5.2 1.1 - - - -
307A HIS* 5.8 4.3 - - + +
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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
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219A ASN* 4.2 4.0 - - - +
221A VAL* 3.6 43.3 - - + -
222A LEU* 4.1 17.7 - - + -
247A PHE* 3.2 16.5 - - + -
255A ILE* 4.6 1.3 - - + -
275A MET* 3.9 16.6 - - + -
297A TRP* 2.8 49.2 + - + +
298A LEU* 3.9 4.0 - - - +
300A ALA* 1.3 73.8 - - - +
302A CYS* 1.3 57.3 + - - +
303A ARG 3.0 0.2 - - - -
304A GLY* 2.9 35.4 + - - -
305A ILE 3.2 6.0 + - - +
306A GLU* 3.8 16.8 - - + -
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Residues in contact with CYS 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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243A VAL* 4.4 2.6 - - - +
247A PHE* 3.5 23.8 - - - +
275A MET* 3.6 14.2 - - + +
276A GLY* 5.0 0.7 - - - -
278A LEU* 3.5 39.3 - - + -
279A THR* 3.7 24.2 - - + +
286A LEU* 5.5 0.2 - - - -
298A LEU 3.0 13.8 + - - +
299A TYR* 3.4 7.4 - - - -
300A ALA 3.3 0.2 - - - -
301A MET* 1.3 77.9 - - - +
303A ARG* 1.3 84.6 + - - +
304A GLY 3.4 1.1 - - - -
504A GOL 4.9 4.3 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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