Contacts of the helix formed by residues 2255 - 2267 (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 GLY2255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A TRP* 3.3 24.5 - - - -
2254A GLY* 1.3 70.9 - - - -
2256A SER* 1.3 62.3 + - - +
2257A TRP 3.2 1.3 + - - -
2258A ARG* 3.6 6.3 + - - +
2259A LYS* 3.4 34.7 + - - +
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Residues in contact with SER2256 (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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3A LEU* 4.6 20.4 - - - -
2254A GLY* 3.3 1.6 - - - -
2255A GLY* 1.3 75.6 + - - +
2257A TRP* 1.3 72.7 + - - +
2258A ARG 3.5 0.2 - - - -
2259A LYS* 3.8 13.2 - - - +
2260A LEU* 3.0 30.7 + - - +
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Residues in contact with TRP2257 (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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2239A PRO* 4.7 2.6 - - - +
2243A SER* 3.7 23.4 + - - -
2253A LEU* 4.2 18.2 - - + +
2254A GLY* 3.4 36.8 - - - +
2255A GLY 3.2 0.8 - - - -
2256A SER* 1.3 84.8 + - - +
2258A ARG* 1.3 59.5 + - - +
2260A LEU* 3.6 21.7 + - + +
2261A GLY* 3.2 21.3 + - - -
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Residues in contact with ARG2258 (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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171A LEU 3.0 22.0 + - - -
172A GLU* 3.4 15.8 + - - +
173A ALA 3.0 26.8 + - - -
174A TRP* 3.7 38.7 - - + +
175A ASP* 4.9 5.3 + - - -
2240A TYR* 3.2 32.4 + - + -
2243A SER* 3.4 26.2 - - - +
2244A ASN* 3.0 29.5 + - - +
2247A SER* 4.5 1.6 - - - -
2253A LEU* 5.3 0.7 - - + -
2254A GLY 4.7 0.6 + - - -
2255A GLY 3.6 8.1 + - - +
2256A SER 3.5 0.2 - - - -
2257A TRP* 1.3 75.9 - - - +
2259A LYS* 1.3 64.9 + - + +
2261A GLY* 3.3 1.2 + - - -
2262A LEU* 3.1 32.2 + - + +
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Residues in contact with LYS2259 (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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8A SER* 5.8 2.5 - - - +
12A TYR* 4.1 1.0 + - - -
69A SER* 4.8 8.9 + - - +
172A GLU* 2.8 53.4 + - + +
2255A GLY* 3.4 26.9 + - - +
2256A SER* 3.8 9.9 - - - +
2257A TRP 3.3 0.4 - - - -
2258A ARG* 1.3 76.2 - - + +
2260A LEU* 1.3 64.3 + - - +
2262A LEU* 3.5 13.0 + - + +
2263A ILE* 3.3 29.6 + - + +
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Residues in contact with LEU2260 (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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2239A PRO* 5.6 7.0 - - + -
2256A SER 3.0 18.3 + - - +
2257A TRP* 3.8 25.8 - - + +
2259A LYS* 1.3 75.3 - - - +
2261A GLY* 1.3 58.4 + - - +
2263A ILE* 3.0 20.6 + - + +
2264A THR* 2.9 45.5 + - + +
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Residues in contact with GLY2261 (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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2236A CYS 3.8 0.9 - - - +
2239A PRO* 4.1 4.9 - - - -
2240A TYR* 3.7 35.3 - - - +
2257A TRP 3.2 11.7 + - - -
2258A ARG 3.3 4.4 + - - -
2260A LEU* 1.3 77.9 - - - +
2262A LEU* 1.3 56.5 + - - +
2264A THR* 3.0 10.0 + - - -
2265A GLY* 2.9 26.7 + - - -
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Residues in contact with LEU2262 (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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12A TYR* 3.2 19.6 - - - +
62A LYS* 4.4 20.6 - - - -
86A HIS* 4.7 11.0 + - - +
87A PHE* 3.7 31.9 - - + -
90A LEU* 6.1 2.4 - - + +
171A LEU* 4.1 26.2 - - + +
172A GLU* 4.6 13.5 - - - +
2240A TYR* 3.8 15.9 - - + -
2258A ARG* 3.1 23.2 + - + +
2259A LYS* 3.7 12.6 - - + +
2260A LEU 3.2 0.2 - - - -
2261A GLY* 1.3 74.9 - - - +
2263A ILE* 1.3 57.9 + - - +
2265A GLY* 4.0 1.1 - - - -
2266A ALA* 3.1 26.9 + - - +
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Residues in contact with ILE2263 (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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8A SER* 3.5 31.2 - - - +
11A LEU* 4.0 37.0 - - + -
12A TYR* 3.6 26.9 - - + +
2259A LYS* 3.3 20.4 + - + +
2260A LEU* 3.0 18.2 + - + +
2262A LEU* 1.3 74.7 - - - +
2264A THR* 1.3 69.4 + - + +
2266A ALA* 3.2 13.2 + - - +
2267A TRP* 3.2 21.6 + - + -
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Residues in contact with THR2264 (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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2235A LEU 3.2 22.1 + - - +
2236A CYS* 3.1 26.6 + - - +
2239A PRO* 3.6 9.1 - - + +
2260A LEU* 2.9 40.9 + - + +
2261A GLY* 3.0 15.6 + - - -
2263A ILE* 1.3 73.5 - - + +
2265A GLY* 1.3 63.5 + - - +
2267A TRP* 3.1 21.0 + - - +
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Residues in contact with GLY2265 (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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55A LEU* 4.4 0.3 - - - +
90A LEU* 3.2 26.4 - - - +
2236A CYS 3.1 18.8 - - - -
2237A VAL* 4.7 1.3 - - - -
2240A TYR* 6.1 0.4 - - - -
2261A GLY 2.9 16.9 + - - -
2262A LEU* 4.0 1.6 - - - -
2263A ILE 3.2 0.2 - - - -
2264A THR* 1.3 74.6 + - - +
2266A ALA* 1.3 57.3 - - - +
2268A SER* 2.8 29.3 + - - -
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Residues in contact with ALA2266 (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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12A TYR* 3.7 25.4 - - + -
15A ALA* 4.0 7.3 - - + +
55A LEU* 5.2 4.3 - - - -
59A LEU* 3.9 24.0 - - + +
86A HIS* 5.1 5.3 - - + -
90A LEU* 5.4 0.6 - - - +
2262A LEU 3.1 15.8 + - - +
2263A ILE 3.4 9.9 - - - +
2265A GLY* 1.3 75.0 - - - +
2267A TRP* 1.3 57.6 + - + +
2268A SER 3.1 5.4 + - - -
2269A VAL* 3.2 27.4 + - - +
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Residues in contact with TRP2267 (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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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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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