Contacts of the helix formed by residues 4213 - 4218 (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 ASN4213 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3195A ILE 4.4 14.1 - - - +
3196A ARG* 4.5 1.6 - - - -
3197A MET* 3.6 30.8 - - - +
4212A GLY* 1.3 72.9 - - - -
4214A ALA* 1.3 64.9 + - - +
4215A LEU 3.4 2.2 - - - -
4216A LYS* 2.9 45.3 + - - +
4217A PHE* 3.2 22.9 - - + -
1013B T 2.6 49.1 + - - +
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Residues in contact with ALA4214 (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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3196A ARG* 3.6 24.0 - - - +
4168A ALA 5.1 1.1 + - - +
4171A MET* 4.2 5.2 - - + +
4172A SER* 3.5 37.2 - - - +
4175A MET* 3.8 13.5 - - + -
4211A GLY 4.9 0.2 + - - -
4212A GLY 3.7 0.6 - - - -
4213A ASN* 1.3 77.0 - - - +
4215A LEU* 1.3 64.2 + - - +
4217A PHE* 3.1 13.3 + - - +
4218A TYR* 3.2 19.4 + - + -
1013B T 4.1 2.4 + - - -
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Residues in contact with LEU4215 (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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4061A ILE* 3.7 30.3 - - + -
4063A GLU* 3.5 41.7 - - + +
4146A VAL* 4.3 13.0 - - + -
4171A MET* 5.6 8.5 - - + +
4175A MET* 3.9 19.9 - - + +
4191A PHE* 3.7 28.3 - - + -
4193A ASN* 4.5 2.9 - - - +
4209A THR* 5.9 3.1 - - + -
4210A THR 5.7 0.4 - - - +
4211A GLY 5.3 5.9 + - - +
4212A GLY 5.1 3.0 + - - +
4213A ASN 3.4 0.8 - - - -
4214A ALA* 1.3 76.7 - - - +
4216A LYS* 1.3 66.1 + - - +
4218A TYR 4.5 0.4 - - - +
4219A ALA* 2.9 31.9 + - + +
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Residues in contact with LYS4216 (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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3068A GLU* 3.3 36.0 - - + +
4063A GLU* 4.6 0.8 + - - -
4208A THR* 4.3 21.2 - - - +
4209A THR* 4.9 12.7 + - + +
4212A GLY 4.2 9.9 + - - +
4213A ASN* 2.9 41.5 + - + +
4214A ALA 3.3 0.4 + - - -
4215A LEU* 1.3 78.1 - - - +
4217A PHE* 1.3 54.3 + - + +
4219A ALA 4.1 1.2 + - - -
4222A ARG* 4.0 36.9 - - - +
4248A LYS* 2.7 36.4 + - - +
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Residues in contact with PHE4217 (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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3066A GLY 3.3 17.9 - - - -
3067A PRO* 3.3 6.3 - - + -
3068A GLU* 3.1 34.1 - - + -
3072A LYS* 3.9 2.7 - - - -
3096A GLU* 4.5 1.7 - - - +
3194A GLN* 3.5 43.5 - - + +
3195A ILE* 3.5 35.9 - - + -
3196A ARG* 3.9 2.2 - - - -
3501A ALF 3.2 31.1 - - - -
4213A ASN* 3.2 26.9 - - + -
4214A ALA 3.1 6.6 + - - +
4215A LEU 3.0 0.4 - - - -
4216A LYS* 1.3 80.6 - - + +
4218A TYR* 1.3 62.3 + - + +
4219A ALA 3.6 0.9 - - - +
4248A LYS* 2.8 20.1 + - - +
4250A LYS* 3.8 5.5 + - - -
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Residues in contact with TYR4218 (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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3096A GLU* 4.6 15.0 - - + -
3098A ALA* 5.7 1.9 - - - +
3147A ALA* 3.2 26.7 + - - +
3148A ALA* 3.3 22.1 - - + -
3194A GLN* 3.7 26.7 - - - -
3196A ARG* 3.9 9.8 + - - -
4061A ILE* 4.1 24.7 + - + +
4172A SER 5.1 1.3 - - - -
4175A MET* 3.4 45.1 - - + -
4176A ARG* 3.6 9.6 - - - +
4179A ALA* 4.0 22.9 - - + -
4214A ALA* 3.2 24.1 + - + +
4215A LEU 4.3 0.9 - - - +
4217A PHE* 1.3 77.4 - - - +
4219A ALA* 1.3 65.9 + - - +
4220A SER* 3.4 7.3 + - - -
4250A LYS* 4.7 5.1 + - - +
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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