Contacts of the helix formed by residues 298 - 310 (chain C) in PDB entry 1KEV
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 298 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96A GLN* 4.3 0.4 - - - -
84C PRO* 3.8 13.8 - - - +
86C THR 3.1 12.9 + - - -
88C PRO* 4.2 0.8 - - - +
90C TRP* 4.1 11.9 - - - -
131C MET 3.9 1.3 - - - -
132C ASN* 3.4 21.7 + - - -
297C GLY* 1.3 77.1 - - - +
299C ARG* 1.3 64.9 + - - -
300C LEU 3.6 0.7 - - - -
302C ALA* 3.4 19.8 + - - +
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Residues in contact with ARG 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 4.0 26.4 - - + +
96A GLN* 3.6 6.1 + - - +
74C ASP* 3.1 38.0 + - - +
75C PHE* 4.2 10.3 - - - -
130C ASP 3.1 23.4 + - - -
131C MET* 2.9 26.5 + - - +
132C ASN* 4.0 0.4 - - - +
133C LEU 3.0 29.4 + - - +
298C GLY* 1.3 69.0 - - - -
300C LEU* 1.3 61.6 + - - +
302C ALA* 3.2 6.0 + - - +
303C GLU* 2.9 57.3 + - + +
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.8 24.4 - - + +
96A GLN* 3.1 25.6 + - + +
97A ALA* 3.8 41.1 - - + +
299C ARG* 1.3 77.5 - - - +
301C ARG* 1.3 63.3 + - - +
303C GLU* 3.3 13.2 + - + +
304C MET* 3.0 55.3 + - + +
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Residues in contact with ARG 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A GLN* 4.7 0.2 + - - -
166B MET* 5.0 6.7 + - - +
100C GLN* 5.4 0.9 - - - +
153C THR* 3.1 41.6 + - - +
156C PHE* 4.1 5.3 - - - +
157C HIS* 3.8 9.5 - - - +
160C GLU* 3.1 40.1 + - - -
296C PRO* 3.8 34.6 - - + +
297C GLY* 3.4 24.2 + - - +
298C GLY 3.9 0.6 + - - -
299C ARG 3.4 0.4 - - - -
300C LEU* 1.3 77.5 - - - +
302C ALA* 1.3 62.6 + - - +
304C MET* 4.0 8.0 - - - +
305C LEU* 3.1 55.4 + - + +
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Residues in contact with ALA 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ILE* 5.1 10.8 - - + +
84C PRO* 4.8 18.1 - - + +
134C ALA* 3.7 21.2 - - + +
148C ILE* 4.6 9.2 - - + +
298C GLY 3.4 13.2 + - - +
299C ARG* 3.2 10.0 + - - +
301C ARG* 1.3 80.8 - - - +
303C GLU* 1.3 56.8 + - - +
305C LEU* 4.0 4.3 - - - +
306C ARG* 3.0 29.5 + - - +
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Residues in contact with GLU 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A LEU* 4.7 10.7 - - - +
75C PHE* 5.8 0.3 - - - -
134C ALA* 4.0 17.7 - - + +
135C ILE 5.2 0.7 + - - -
299C ARG* 2.9 54.7 + - - +
300C LEU* 3.9 12.2 - - + +
302C ALA* 1.3 73.2 - - - +
304C MET* 1.3 62.2 + - + +
306C ARG* 3.5 31.3 + - - +
307C ASP* 3.0 37.7 + - - +
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Residues in contact with MET 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B GLN* 4.7 14.6 - - + +
166B MET 3.6 24.2 - - - +
167B GLY* 3.8 14.8 - - - +
168B SER* 3.9 27.8 - - - +
237B ASP* 5.1 6.5 - - - +
300C LEU* 3.0 49.3 + - + +
301C ARG* 4.0 8.3 - - - +
303C GLU* 1.3 75.9 - - + +
305C LEU* 1.3 64.1 + - + +
307C ASP* 3.5 6.7 + - - +
308C MET* 3.3 24.3 + - - +
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Residues in contact with LEU 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B MET* 4.8 6.3 - - + +
148C ILE* 4.1 18.4 - - + +
152C MET* 3.7 19.0 - - + +
153C THR* 3.7 38.6 - - - +
156C PHE* 4.1 24.9 - - + -
301C ARG* 3.1 46.1 + - + +
302C ALA* 4.1 1.1 - - - +
304C MET* 1.3 73.9 - - + +
306C ARG* 1.3 66.8 + - - +
308C MET* 3.0 23.4 + - - +
309C VAL* 3.2 16.4 + - - +
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Residues in contact with ARG 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C ILE* 4.2 14.8 - - + -
134C ALA* 4.4 1.6 - - - +
135C ILE* 3.0 46.0 + - - +
137C PRO* 3.6 30.4 - - + +
140C MET* 4.3 4.2 - - + +
148C ILE* 4.2 13.6 - - + +
302C ALA 3.0 20.3 + - - +
303C GLU* 3.5 38.2 + - - +
305C LEU* 1.3 76.2 - - - +
307C ASP* 1.3 84.4 + - - +
309C VAL* 3.1 8.0 + - - +
310C VAL* 3.0 20.6 + - + +
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Residues in contact with ASP 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167B GLY 5.4 5.3 - - - +
192B GLY* 5.3 2.5 - - - -
193B ARG 6.1 0.2 - - - +
303C GLU* 3.0 18.6 + - - +
304C MET* 3.8 7.9 - - - +
306C ARG* 1.3 101.8 + - - +
308C MET* 1.3 66.1 + - - +
310C VAL* 3.2 10.6 + - - +
311C TYR* 2.9 47.1 + - + -
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Residues in contact with MET 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B MET* 3.8 24.7 - - + +
167B GLY* 3.7 26.0 - - - -
190B GLY* 3.4 20.6 - - - +
192B GLY* 4.6 7.6 - - - -
152C MET* 4.2 6.5 - - + -
156C PHE* 3.9 27.4 - - + -
188C LEU* 4.1 13.9 - - + -
304C MET 3.3 12.4 + - - +
305C LEU* 3.0 18.4 + - - +
307C ASP* 1.3 76.5 - - - +
309C VAL* 1.3 59.4 + - - +
311C TYR* 3.4 1.9 + - - -
312C ASN 3.4 3.5 + - - -
313C ARG* 3.0 48.4 + - + +
314C VAL* 5.0 2.5 - - + -
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Residues in contact with VAL 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C MET* 3.7 24.2 - - + -
144C ASN* 5.9 4.3 - - + +
148C ILE* 4.2 9.4 - - + -
152C MET* 4.0 14.6 - - + -
305C LEU 3.5 13.7 - - - +
306C ARG 3.1 7.8 + - - +
308C MET* 1.3 74.7 - - - +
310C VAL* 1.3 64.1 + - - +
312C ASN* 3.0 20.1 + - - -
314C VAL* 4.4 18.2 - - + +
316C LEU* 3.9 33.0 - - + +
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Residues in contact with VAL 310 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137C PRO* 4.3 18.4 - - + -
140C MET* 4.1 16.8 - - + -
306C ARG* 3.0 18.8 + - + +
307C ASP* 3.2 15.5 + - - +
309C VAL* 1.3 75.4 - - - +
311C TYR* 1.3 75.0 + - + +
312C ASN* 3.2 10.8 + - - +
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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