Contacts of the helix formed by residues 2100 - 2107 (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 ASP2100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2098A ALA 3.5 3.2 + - - +
2099A LEU* 1.3 76.7 - - - +
2101A PRO* 1.3 74.2 - - - +
2102A ILE* 3.2 19.8 + - - +
2103A TYR* 3.0 26.8 + - + +
2104A ALA* 2.9 21.5 + - - +
2502A ADP 3.6 8.7 + - - +
3037A VAL* 4.1 18.6 + - + +
3060A ARG* 4.6 9.2 - - - +
3250A LYS 4.2 14.5 - - - +
3251A ILE* 4.1 11.0 - - + +
3330A ASN* 5.6 1.9 + - - -
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Residues in contact with PRO2101 (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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2099A LEU* 3.4 11.6 - - - +
2100A ASP* 1.3 87.2 - - - +
2102A ILE* 1.3 70.3 + - + +
2104A ALA* 3.1 4.5 + - + +
2105A ARG* 2.9 26.0 + - - +
2111A ILE* 3.5 16.3 - - + +
3029A LEU* 3.7 35.9 - - + +
3030A GLY* 6.0 0.2 - - - -
3032A ASP 5.7 0.2 - - - +
3035A MET* 3.5 36.8 - - + +
3036A ASP* 4.6 6.3 - - - +
3037A VAL 5.8 0.2 - - - +
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Residues in contact with ILE2102 (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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2100A ASP* 3.2 14.1 + - - +
2101A PRO* 1.3 92.7 - - + +
2103A TYR* 1.3 62.9 + - - +
2105A ARG* 3.4 31.4 + - - +
2106A LYS* 3.1 42.6 + - - +
3036A ASP* 4.6 14.4 - - - +
3037A VAL 6.0 0.9 - - - +
3330A ASN* 5.0 5.6 - - - +
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Residues in contact with TYR2103 (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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2074A THR* 3.9 17.5 + - - +
2077A LEU* 4.9 7.0 - - + -
2100A ASP* 3.0 17.7 + - + +
2102A ILE* 1.3 78.0 - - - +
2104A ALA* 1.3 66.9 + - - +
2106A LYS* 3.0 15.0 + - + +
2107A LEU* 3.0 54.2 + - + +
2262A ILE* 4.9 2.4 - - - +
2263A LEU 4.7 1.0 + - - -
2264A TYR* 4.1 4.3 - - - -
2265A GLY* 3.3 37.7 + - - -
2502A ADP 3.1 75.1 + + - +
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Residues in contact with ALA2104 (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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2077A LEU* 4.2 33.4 - - + +
2099A LEU* 4.5 6.3 - - + -
2100A ASP 2.9 12.0 + - - +
2101A PRO* 3.1 12.3 + - + +
2103A TYR* 1.3 78.1 - - - +
2105A ARG* 1.3 60.5 + - - +
2107A LEU* 3.2 9.1 + - - +
2108A GLY 3.4 0.2 + - - -
2109A VAL* 3.0 27.6 + - + +
2111A ILE* 3.6 16.2 - - + -
2114A LEU* 6.3 0.4 - - + -
3029A LEU* 4.6 3.6 - - + -
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Residues in contact with ARG2105 (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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2101A PRO 2.9 8.6 + - - +
2102A ILE* 3.5 33.3 + - - +
2104A ALA* 1.3 76.8 - - - +
2106A LYS* 1.3 55.4 + - - +
2108A GLY* 2.8 25.6 + - - -
2109A VAL 3.7 13.4 + - - +
2111A ILE* 3.5 27.1 - - + +
2112A ASP* 5.9 1.2 + - - -
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Residues in contact with LYS2106 (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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2102A ILE* 3.1 28.8 + - - +
2103A TYR* 3.0 21.0 + - + +
2105A ARG* 1.3 76.9 - - - +
2107A LEU* 1.3 58.5 + - - +
2108A GLY* 3.3 3.5 + - - -
2265A GLY* 3.6 37.8 - - - +
2266A GLU* 3.9 5.9 - - - +
3329A SER 4.9 4.0 + - - -
3330A ASN* 3.2 28.7 - - - +
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Residues in contact with LEU2107 (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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2074A THR* 3.9 20.6 - - + +
2077A LEU* 3.8 29.6 - - + -
2078A GLN* 2.9 25.2 + - - +
2081A ALA* 3.9 6.3 - - - +
2085A ARG* 5.5 0.9 + - - -
2103A TYR* 3.0 52.5 + - + +
2104A ALA* 3.6 7.6 - - - +
2105A ARG 3.1 0.6 - - - -
2106A LYS* 1.3 76.0 - - - +
2108A GLY* 1.3 59.5 + - - +
2109A VAL* 3.5 5.8 + - + -
2266A GLU 3.7 10.6 - - - +
2267A GLY* 3.5 33.9 - - - +
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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