Contacts of the helix formed by residues 2267 - 2277 (chain A) in PDB entry 5KW2
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 TRP2267 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A LEU* 2.8 40.7 + - + +
12A TYR* 5.6 0.2 - - - -
14A ALA* 3.8 22.4 - - + -
15A ALA* 3.7 11.9 - - + -
18A LEU* 3.8 20.4 - - + -
2236A CYS* 4.2 4.7 - - - -
2263A ILE* 3.2 28.0 + - + +
2264A THR* 3.1 16.3 + - - +
2266A ALA* 1.3 72.4 - - + +
2268A SER* 1.3 58.3 + - - +
2269A VAL 3.1 2.0 - - - -
2270A VAL* 2.9 57.1 + - + +
2271A LEU* 3.1 26.7 + - + +
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Residues in contact with SER2268 (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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52A ASP* 5.0 0.4 + - - -
55A LEU* 3.7 8.8 - - - +
90A LEU* 3.6 15.3 + - - +
2232A THR 5.4 0.2 - - - -
2236A CYS* 3.8 23.1 - - - -
2237A VAL* 5.1 4.7 - - - -
2264A THR 3.6 2.8 + - - -
2265A GLY 2.8 21.0 + - - -
2266A ALA 3.1 0.2 - - - -
2267A TRP* 1.3 77.4 - - - +
2269A VAL* 1.3 57.0 + - - +
2270A VAL 3.1 0.4 - - - -
2271A LEU* 4.3 1.6 - - - +
2272A ASN* 2.7 58.5 + - - +
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Residues in contact with VAL2269 (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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15A ALA 3.3 29.6 - - - +
19A GLY* 3.8 8.8 - - - -
22A LEU* 4.9 0.2 - - - +
23A ASN* 2.9 27.1 + - - +
52A ASP* 3.4 34.3 - - - +
55A LEU* 3.7 29.8 - - + -
56A THR* 3.5 14.6 - - - +
59A LEU* 4.4 4.9 - - + -
2266A ALA 3.2 14.8 - - - +
2268A SER* 1.3 76.4 + - - +
2270A VAL* 1.3 58.7 + - + +
2273A PRO* 3.2 10.7 - - - +
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Residues in contact with VAL2270 (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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15A ALA* 3.9 25.4 - - - +
18A LEU* 3.9 21.8 - - + -
19A GLY 4.3 0.9 - - - +
22A LEU* 4.0 20.7 - - + +
2267A TRP* 2.9 42.5 + - + +
2269A VAL* 1.3 82.5 - - + +
2271A LEU* 1.3 66.3 + - + +
2272A ASN 3.5 0.2 - - - -
2273A PRO* 3.4 13.4 - - - +
2274A LEU* 3.5 21.4 - - + +
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Residues in contact with LEU2271 (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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2232A THR* 3.6 34.1 - - + -
2235A LEU* 6.2 4.9 - - + -
2236A CYS* 3.9 21.1 - - - -
2267A TRP* 3.1 36.4 + - + +
2268A SER* 4.3 1.8 - - - +
2270A VAL* 1.3 81.9 - - + +
2272A ASN* 1.3 67.6 + - - +
2274A LEU* 2.9 31.2 + - + +
2275A VAL* 3.4 9.5 + - + +
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Residues in contact with ASN2272 (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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48A LEU* 3.5 37.0 - - + +
52A ASP* 3.4 23.9 + - - +
90A LEU 5.7 0.2 + - - -
93A GLY* 3.9 15.4 + - - -
97A LEU* 3.4 23.3 - - - +
2232A THR* 4.0 7.8 + - - +
2268A SER* 2.7 43.4 + - - +
2271A LEU* 1.3 71.3 - - - +
2273A PRO* 1.4 61.8 - - - +
2274A LEU 3.2 0.7 + - - -
2275A VAL* 3.3 24.7 - - - +
2276A THR* 3.8 2.1 - - - +
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Residues in contact with PRO2273 (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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22A LEU* 4.0 28.5 - - + +
23A ASN* 3.6 17.0 - - - +
26A ALA* 4.1 11.6 - - + +
48A LEU* 5.1 1.6 - - + -
52A ASP* 3.4 12.5 - - - +
2269A VAL 3.2 27.4 - - - +
2270A VAL 3.4 12.1 - - - +
2272A ASN* 1.4 90.0 - - + +
2274A LEU* 1.3 59.1 + - + +
2275A VAL 3.4 0.2 - - - -
2276A THR* 3.0 23.3 + - + +
2277A GLY 4.0 2.6 + - - -
2278A TYR 4.7 4.7 + - - -
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Residues in contact with LEU2274 (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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22A LEU* 4.9 19.3 - - + -
2270A VAL* 3.5 27.6 - - + +
2271A LEU* 2.9 21.1 + - + +
2273A PRO* 1.3 80.3 - - + +
2275A VAL* 1.3 62.8 + - + +
2276A THR 3.4 0.5 + - - -
2277A GLY* 3.6 11.3 + - - -
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Residues in contact with VAL2275 (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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97A LEU* 3.5 26.5 - - + -
100A LEU* 4.7 5.4 - - + -
2225A VAL* 3.6 28.8 - - - +
2228A GLY* 3.6 36.6 - - - +
2229A ALA* 4.3 5.6 - - + +
2232A THR* 3.8 13.2 - - + +
2271A LEU* 3.7 11.9 - - + +
2272A ASN 3.3 15.5 - - - +
2274A LEU* 1.3 76.3 - - + +
2276A THR* 1.3 67.2 + - + +
2277A GLY* 3.4 0.6 + - - -
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Residues in contact with THR2276 (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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26A ALA* 5.3 4.0 - - - +
45A ALA* 3.9 17.0 - - + +
48A LEU* 3.8 28.9 - - + -
100A LEU* 3.9 24.2 - - + -
104A ARG* 4.7 6.9 + - - -
2225A VAL* 4.7 7.8 - - - +
2272A ASN 3.8 4.0 - - - +
2273A PRO* 3.0 17.9 + - + +
2275A VAL* 1.3 79.5 - - + +
2277A GLY* 1.3 60.4 + - - +
2278A TYR* 3.5 37.2 + - - +
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Residues in contact with GLY2277 (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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2273A PRO 4.0 1.4 + - - -
2274A LEU 3.6 11.2 + - - -
2275A VAL 3.4 3.0 - - - -
2276A THR* 1.3 80.9 + - - +
2278A TYR* 1.3 66.8 + - - +
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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