Contacts of the helix formed by residues 2237 - 2249 (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 VAL2237 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A LEU* 3.6 48.7 - - + +
91A TYR* 5.3 6.7 - - + -
94A GLY* 5.0 6.5 - - - +
97A LEU* 6.2 0.7 - - + -
191A PHE* 3.6 20.0 - - + -
2232A THR 4.5 1.1 - - - +
2233A LEU* 3.3 36.3 - - + +
2236A CYS* 1.3 76.3 - - + +
2238A GLY* 1.3 60.7 + - - +
2239A PRO 3.7 0.2 - - - -
2240A TYR* 4.0 4.8 + - - +
2241A ASN* 2.8 36.0 + - - +
2265A GLY* 4.7 1.8 - - - -
2268A SER* 5.0 6.1 - - - +
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Residues in contact with GLY2238 (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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191A PHE* 3.2 25.6 - - - -
2233A LEU 2.9 13.3 + - - -
2234A LEU* 3.4 7.2 - - - -
2237A VAL* 1.3 75.7 - - - +
2239A PRO* 1.4 70.0 - - - +
2240A TYR 3.2 0.3 + - - -
2241A ASN* 3.3 4.5 + - - +
2242A ALA* 3.1 25.2 + - - +
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Residues in contact with PRO2239 (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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2234A LEU 3.2 13.9 - - - +
2235A LEU* 3.3 25.1 - - + +
2236A CYS 3.4 8.5 - - - +
2238A GLY* 1.4 88.6 - - - +
2240A TYR* 1.3 61.1 + - - +
2242A ALA* 3.6 6.4 + - + +
2243A SER* 3.1 25.2 + - - -
2257A TRP 4.7 1.9 - - - +
2260A LEU* 5.4 7.0 - - + -
2261A GLY* 4.1 9.0 - - - +
2264A THR* 3.6 16.8 - - + +
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Residues in contact with TYR2240 (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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87A PHE* 3.7 34.6 - + - -
90A LEU* 6.2 2.7 - - + -
91A TYR* 4.6 7.4 - + - -
142A PHE* 5.5 4.2 - - - -
171A LEU 5.1 0.2 + - - -
175A ASP* 4.8 2.6 + - - -
183A ARG* 5.6 1.0 + - - -
187A SER* 5.9 0.2 - - - -
2236A CYS 5.3 0.2 - - - +
2237A VAL* 4.0 8.2 + - - +
2238A GLY 3.3 1.0 - - - -
2239A PRO* 1.3 80.0 - - - +
2241A ASN* 1.3 65.9 + - - +
2243A SER* 2.8 7.3 + - - -
2244A ASN* 2.7 59.6 + - + +
2258A ARG* 3.2 55.0 + - + -
2261A GLY* 3.7 21.3 + - - +
2262A LEU* 3.8 25.4 - - + -
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Residues in contact with ASN2241 (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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91A TYR* 2.6 40.8 + - - -
187A SER* 2.6 32.4 + - - +
191A PHE* 3.8 30.9 - - + +
192A PHE* 4.2 3.8 - - + -
2237A VAL* 2.8 26.1 + - - +
2238A GLY 3.3 2.5 + - - +
2240A TYR* 1.3 85.3 - - - +
2242A ALA* 1.3 61.9 + - - +
2244A ASN* 4.4 1.8 - - - +
2245A VAL* 3.2 27.4 + - - +
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Residues in contact with ALA2242 (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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191A PHE* 6.0 0.2 - - + -
192A PHE* 4.3 13.1 - - + -
2238A GLY 3.1 17.3 + - - +
2239A PRO* 3.8 8.1 - - + +
2241A ASN* 1.3 76.8 - - - +
2243A SER* 1.3 56.7 + - - +
2245A VAL* 3.3 13.1 - - - +
2246A ALA* 3.2 20.1 - - - +
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Residues in contact with SER2243 (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 3.1 14.9 + - - -
2240A TYR* 2.8 18.1 + - - -
2242A ALA* 1.3 76.7 - - - +
2244A ASN* 1.3 58.9 + - - +
2245A VAL 3.4 0.4 - - - -
2246A ALA* 3.4 9.4 + - - -
2247A SER* 3.1 21.8 + - - -
2253A LEU* 3.4 13.2 - - - +
2257A TRP* 3.7 26.9 + - - -
2258A ARG* 3.4 24.7 - - - +
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Residues in contact with ASN2244 (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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175A ASP* 3.6 16.7 + - - +
183A ARG* 3.8 31.5 + - - +
187A SER* 5.0 5.0 + - - +
2240A TYR* 2.7 47.7 + - + +
2241A ASN* 4.2 4.3 - - - +
2242A ALA 3.5 0.2 - - - -
2243A SER* 1.3 72.4 + - - +
2245A VAL* 1.3 62.5 + - - +
2247A SER* 2.5 27.1 + - - -
2248A PHE* 3.3 13.5 - - - -
2258A ARG* 3.0 27.3 + - - +
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Residues in contact with VAL2245 (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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184A PHE* 3.4 40.6 - - + +
187A SER* 5.0 5.9 + - - -
192A PHE* 4.6 15.3 - - + -
2241A ASN 3.2 19.6 + - - +
2242A ALA* 3.3 12.8 - - - +
2244A ASN* 1.3 73.2 - - - +
2246A ALA* 1.3 62.1 + - + +
2247A SER 3.0 8.5 + - - -
2248A PHE* 3.4 21.1 + - + +
2249A LEU* 3.7 23.0 + - + +
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Residues in contact with ALA2246 (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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2242A ALA 3.2 17.9 - - - +
2243A SER* 3.4 11.1 + - - +
2244A ASN 3.3 0.6 - - - -
2245A VAL* 1.3 79.0 - - + +
2247A SER* 1.3 51.7 + - - +
2249A LEU* 2.7 26.3 - - - +
2250A TYR* 3.8 24.0 - - + +
2253A LEU* 3.3 20.3 - - + +
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Residues in contact with SER2247 (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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174A TRP* 3.6 34.2 - - - -
175A ASP 5.3 4.4 + - - -
2243A SER 3.1 10.1 + - - -
2244A ASN* 2.5 28.5 + - - -
2245A VAL 3.0 1.4 - - - -
2246A ALA* 1.3 77.3 - - - +
2248A PHE* 1.3 70.5 + - - +
2249A LEU 3.1 11.5 - - - +
2250A TYR 3.9 8.4 - - - +
2251A PRO* 4.6 4.7 - - - +
2253A LEU* 3.8 4.9 - - - -
2258A ARG* 4.5 1.1 - - - -
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Residues in contact with PHE2248 (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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175A ASP* 3.6 33.4 - - + -
176A PRO 3.5 23.1 - - - -
177A ALA* 4.1 20.5 - - + +
180A GLY* 3.6 31.6 - - - -
183A ARG* 3.7 30.7 - - + -
184A PHE* 4.7 3.6 - - + -
2244A ASN* 3.3 29.6 - - - -
2245A VAL* 3.4 14.3 + - + +
2247A SER* 1.3 82.7 - - - +
2249A LEU* 1.3 64.9 - - + +
2251A PRO* 5.3 3.6 - - - +
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Residues in contact with LEU2249 (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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2245A VAL* 3.7 24.3 + - + +
2246A ALA* 2.7 26.6 - - - +
2247A SER 3.1 4.5 - - - -
2248A PHE* 1.3 78.8 - - + +
2250A TYR* 1.3 86.9 + - + +
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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