Contacts of the helix formed by residues 2213 - 2218 (chain A) in PDB entry 3CMT
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 ASN2213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1195A ILE 4.5 14.6 - - - +
1196A ARG* 4.5 2.7 - - - -
1197A MET* 3.6 31.0 - - - +
2212A GLY* 1.3 73.6 - - - -
2214A ALA* 1.3 66.1 + - - +
2215A LEU 3.3 2.7 - - - -
2216A LYS* 2.9 46.2 + - - +
2217A PHE* 3.2 20.6 - - + -
1007B A 2.6 47.2 + - - +
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Residues in contact with ALA2214 (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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1196A ARG* 3.6 24.0 - - - +
2168A ALA 5.1 0.7 - - - +
2171A MET* 4.2 5.4 - - + +
2172A SER* 3.5 37.9 - - - +
2175A MET* 3.8 12.8 - - + -
2211A GLY 4.9 0.6 + - - +
2212A GLY 3.7 0.8 - - - -
2213A ASN* 1.3 76.4 - - - +
2215A LEU* 1.3 65.1 + - - +
2217A PHE* 3.1 13.7 + - - +
2218A TYR* 3.2 19.0 + - + -
1007B A 4.1 2.0 + - - -
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Residues in contact with LEU2215 (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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2061A ILE* 3.6 30.1 - - + -
2063A GLU* 3.4 41.1 - - + +
2146A VAL* 4.3 13.0 - - + -
2171A MET* 5.6 8.2 - - + +
2175A MET* 3.9 19.5 - - + +
2191A PHE* 3.7 28.9 - - + -
2193A ASN* 4.5 2.7 - - - +
2209A THR* 5.6 3.1 - - + -
2210A THR 5.8 1.1 - - - +
2211A GLY 5.3 5.7 + - - +
2212A GLY 5.1 3.5 + - - +
2213A ASN 3.3 1.0 - - - +
2214A ALA* 1.3 78.5 - - - +
2216A LYS* 1.3 63.7 + - - +
2218A TYR 4.5 0.4 - - - +
2219A ALA* 2.9 32.3 + - + +
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Residues in contact with LYS2216 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1068A GLU* 3.3 35.4 - - + +
2063A GLU* 4.6 0.8 + - - -
2208A THR* 4.3 21.2 - - - +
2209A THR* 4.9 12.5 + - + +
2212A GLY 4.2 10.5 + - - +
2213A ASN* 2.9 42.0 + - + +
2214A ALA 3.2 0.4 + - - -
2215A LEU* 1.3 78.3 - - - +
2217A PHE* 1.3 54.1 + - + +
2219A ALA 4.0 1.4 + - - -
2222A ARG* 4.0 34.9 + - - +
2248A LYS* 2.7 36.6 + - - +
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Residues in contact with PHE2217 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1066A GLY 3.4 17.0 - - - -
1067A PRO* 3.5 6.3 - - + -
1068A GLU* 3.2 33.2 - - + -
1072A LYS* 4.0 2.0 - - - -
1096A GLU* 4.5 2.2 - - - +
1194A GLN* 3.4 48.2 - - + +
1195A ILE* 3.4 36.1 - - + -
1196A ARG* 3.8 2.2 - - - -
1501A ALF 3.3 20.2 - - - -
2213A ASN* 3.2 29.2 - - + -
2214A ALA 3.1 5.4 + - - +
2216A LYS* 1.3 81.7 - - + +
2218A TYR* 1.3 61.8 + - + +
2219A ALA 3.6 0.7 - - - +
2248A LYS* 2.8 19.6 + - - +
2250A LYS* 3.8 11.8 + - - -
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Residues in contact with TYR2218 (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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1096A GLU* 4.8 13.5 - - + +
1098A ALA* 5.7 0.9 - - - +
1147A ALA* 3.1 26.3 + - - +
1148A ALA* 3.4 22.4 - - + -
1194A GLN* 3.9 15.3 - - - -
1196A ARG* 3.9 21.6 + - - -
2061A ILE* 4.0 23.8 + - + +
2172A SER 5.1 1.3 - - - -
2175A MET* 3.3 45.8 - - + -
2176A ARG* 3.6 11.2 - - - +
2179A ALA* 4.0 22.0 - - + -
2214A ALA* 3.2 24.1 + - + +
2215A LEU 4.3 0.9 - - - +
2217A PHE* 1.3 77.8 - - + +
2219A ALA* 1.3 65.9 + - - +
2220A SER* 3.4 9.0 + - - -
2250A LYS* 4.7 5.5 + - - +
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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