Contacts of the helix formed by residues 3100 - 3107 (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 ASP3100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3098A ALA 3.5 3.0 + - - +
3099A LEU* 1.3 78.8 - - - +
3101A PRO* 1.4 70.7 - - - +
3102A ILE* 3.2 23.0 + - - +
3103A TYR* 3.0 27.3 + - + +
3104A ALA* 2.9 21.0 + - - +
3502A ADP 3.8 8.3 + - - -
4037A VAL* 3.9 24.9 + - + +
4060A ARG* 4.5 4.9 - - - +
4250A LYS 4.5 13.6 - - - +
4251A ILE* 4.3 9.2 - - - +
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Residues in contact with PRO3101 (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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3099A LEU 3.4 7.1 - - - +
3100A ASP* 1.4 86.7 - - - +
3102A ILE* 1.3 69.5 + - + +
3104A ALA* 3.1 4.3 + - + +
3105A ARG* 2.9 25.8 + - - +
3111A ILE* 3.5 15.9 - - + +
4029A LEU* 3.6 36.6 - - + +
4030A GLY* 5.9 0.2 - - - -
4032A ASP 5.5 0.7 - - - +
4035A MET* 3.3 42.0 - - + +
4036A ASP* 4.4 6.7 - - - +
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Residues in contact with ILE3102 (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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3100A ASP* 3.2 15.4 + - - +
3101A PRO* 1.3 91.1 - - + +
3103A TYR* 1.3 63.4 + - - +
3105A ARG* 3.3 31.1 + - - +
3106A LYS* 3.1 43.4 + - - +
4036A ASP* 4.4 15.9 - - - +
4037A VAL 5.9 1.3 - - - +
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Residues in contact with TYR3103 (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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3074A THR* 3.9 16.8 + - - +
3077A LEU* 4.9 7.0 - - + -
3100A ASP* 3.0 20.8 + - + +
3102A ILE* 1.3 76.9 - - - +
3104A ALA* 1.3 67.2 + - - +
3106A LYS* 3.0 14.5 + - + +
3107A LEU* 3.0 55.9 + - + +
3262A ILE* 4.9 2.3 - - - +
3263A LEU 4.7 1.0 + - - -
3264A TYR* 4.1 4.7 - - - -
3265A GLY* 3.4 37.5 + - - -
3502A ADP 3.3 70.3 + + - +
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Residues in contact with ALA3104 (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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3077A LEU* 4.2 34.7 - - + +
3099A LEU* 4.5 3.1 - - + -
3100A ASP 2.9 10.8 + - - +
3101A PRO* 3.4 11.7 - - + +
3103A TYR* 1.3 77.7 - - - +
3105A ARG* 1.3 61.2 + - - +
3107A LEU* 3.2 8.3 + - - +
3108A GLY 3.4 0.5 + - - -
3109A VAL* 3.0 27.3 + - + +
3111A ILE* 3.6 16.4 - - + -
3114A LEU* 6.3 0.2 - - + -
4029A LEU* 4.4 6.7 - - + -
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Residues in contact with ARG3105 (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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3101A PRO 2.9 8.4 + - - +
3102A ILE* 3.5 33.2 + - - +
3104A ALA* 1.3 73.7 - - - +
3106A LYS* 1.3 62.0 + - - +
3108A GLY* 2.8 22.3 + - - -
3109A VAL 3.7 13.0 - - - +
3111A ILE* 3.5 27.5 - - + +
3112A ASP* 5.9 1.0 + - - -
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Residues in contact with LYS3106 (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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3102A ILE* 3.1 33.9 + - + +
3103A TYR* 3.0 20.5 + - + +
3105A ARG* 1.3 78.0 - - - +
3107A LEU* 1.3 57.5 + - + +
3108A GLY* 3.3 3.5 + - - -
3265A GLY* 3.6 39.1 - - - +
3266A GLU* 4.0 6.4 - - - +
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Residues in contact with LEU3107 (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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3074A THR* 3.9 21.3 - - + +
3077A LEU* 3.8 32.8 - - + -
3078A GLN* 3.0 25.1 + - - +
3081A ALA* 3.9 5.9 - - - +
3085A ARG* 5.5 0.7 + - - -
3103A TYR* 3.0 52.5 + - + +
3104A ALA* 3.6 7.2 - - - +
3105A ARG 3.1 0.8 - - - -
3106A LYS* 1.3 75.4 - - - +
3108A GLY* 1.3 59.5 + - - +
3109A VAL* 3.5 1.3 - - + -
3266A GLU 3.7 10.4 - - - +
3267A GLY* 3.5 33.4 - - - +
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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