Contacts of the helix formed by residues 3100 - 3107 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3098D ALA 3.5 2.6 + - - +
3099D LEU* 1.3 78.7 - - - +
3101D PRO* 1.3 69.9 - - - +
3102D ILE* 3.2 22.0 + - - +
3103D TYR* 3.1 28.8 + - + +
3104D ALA* 2.9 21.3 + - - +
3502D ADP 3.7 9.0 + - - -
4037D VAL* 3.9 21.7 + - + +
4060D ARG* 4.5 3.8 - - - +
4250D LYS 4.1 15.2 - - - +
4251D ILE* 3.8 12.5 - - + +
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Residues in contact with PRO3101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3099D LEU* 3.4 11.4 - - + +
3100D ASP* 1.3 89.3 - - - +
3102D ILE* 1.3 68.0 + - + +
3104D ALA* 3.2 4.1 + - + +
3105D ARG* 3.0 26.9 + - - +
3111D ILE* 3.5 15.1 - - + +
4029D LEU* 3.7 35.4 - - + +
4032D ASP 5.7 0.4 - - - +
4035D MET* 3.4 38.6 - - + +
4036D ASP* 4.6 5.8 - - - +
4037D VAL* 5.1 0.2 - - + -
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Residues in contact with ILE3102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3100D ASP* 3.2 14.7 + - - +
3101D PRO* 1.3 92.7 - - + +
3103D TYR* 1.3 63.6 + - - +
3105D ARG* 3.4 29.8 + - - +
3106D LYS* 3.1 42.7 + - - +
4036D ASP* 4.6 13.7 - - + +
4037D VAL 5.9 2.0 - - - +
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Residues in contact with TYR3103 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3074D THR* 3.9 17.7 + - - +
3077D LEU* 4.9 6.3 - - + -
3100D ASP* 3.1 19.2 + - + +
3102D ILE* 1.3 78.1 - - + +
3104D ALA* 1.3 68.0 + - - +
3106D LYS* 3.0 15.7 + - + +
3107D LEU* 3.0 54.1 + - + +
3262D ILE* 4.9 2.6 - - - +
3263D LEU 4.7 1.2 + - - -
3264D TYR* 4.1 4.5 - - - -
3265D GLY* 3.4 36.8 + - - -
3502D ADP 3.3 72.0 + + - +
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Residues in contact with ALA3104 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3077D LEU* 4.2 34.9 - - + +
3099D LEU* 4.5 4.9 - - + -
3100D ASP 2.9 13.1 + - - +
3101D PRO* 3.2 11.4 + - + +
3103D TYR* 1.3 76.1 - - - +
3105D ARG* 1.3 62.2 + - - +
3107D LEU* 3.2 9.1 + - - +
3109D VAL* 3.1 28.6 + - + +
3111D ILE* 3.6 15.3 - - + -
3114D LEU* 6.3 0.2 - - + -
4029D LEU* 4.6 4.0 - - + -
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Residues in contact with ARG3105 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3101D PRO 3.0 8.4 + - - +
3102D ILE* 3.5 31.8 + - - +
3104D ALA* 1.3 77.4 - - - +
3106D LYS* 1.3 56.4 + - - +
3108D GLY* 2.8 25.5 + - - -
3109D VAL 3.7 13.0 - - - +
3111D ILE* 3.5 27.9 - - + +
3112D ASP* 5.9 1.2 + - - -
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Residues in contact with LYS3106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3102D ILE* 3.1 32.5 + - - +
3103D TYR* 3.0 21.9 + - + +
3105D ARG* 1.3 77.2 - - - +
3107D LEU* 1.3 58.6 + - - +
3108D GLY* 3.3 3.5 + - - -
3265D GLY* 3.5 38.6 - - - +
3266D GLU* 3.9 6.1 - - - +
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Residues in contact with LEU3107 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3074D THR* 3.9 21.1 - - + +
3077D LEU* 3.8 28.9 - - + -
3078D GLN* 3.0 26.3 + - - +
3081D ALA* 3.9 5.9 - - - +
3085D ARG* 5.5 1.0 + - - -
3103D TYR* 3.0 51.8 + - + +
3104D ALA* 3.6 7.6 - - - +
3105D ARG 3.1 0.6 - - - -
3106D LYS* 1.3 75.8 - - - +
3108D GLY* 1.3 58.4 + - - +
3109D VAL* 3.5 5.8 + - + -
3266D GLU 3.7 10.8 - - - +
3267D GLY* 3.5 33.2 - - - +
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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