Contacts of the helix formed by residues 100 - 107 (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 ASP 100 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98D ALA 3.5 2.6 + - - +
99D LEU* 1.3 78.1 - - - +
101D PRO* 1.3 72.2 - - - +
102D ILE* 3.2 20.0 + - - +
103D TYR* 3.0 26.8 + - + +
104D ALA* 2.9 20.8 + - - +
502D ADP 3.7 9.1 + - - +
1037D VAL* 4.1 19.0 + - + +
1060D ARG* 4.6 9.2 - - - +
1250D LYS 4.3 14.3 - - - +
1251D ILE* 4.1 9.9 - - - +
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Residues in contact with PRO 101 (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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99D LEU* 3.4 11.4 - - - +
100D ASP* 1.3 86.8 - - - +
102D ILE* 1.3 68.8 + - + +
104D ALA* 3.2 4.4 + - + +
105D ARG* 2.9 26.2 + - - +
111D ILE* 3.5 16.8 - - + +
1029D LEU* 3.8 35.7 - - + +
1030D GLY* 5.8 0.2 - - - -
1032D ASP 5.6 0.4 - - - +
1035D MET* 3.5 36.8 - - + +
1036D ASP* 4.4 7.9 - - - +
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Residues in contact with ILE 102 (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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100D ASP* 3.2 14.5 + - - +
101D PRO* 1.3 92.6 - - + +
103D TYR* 1.3 57.7 + - - +
105D ARG* 3.4 30.6 + - - +
106D LYS* 3.1 47.3 + - - +
1036D ASP* 4.4 15.3 - - + +
1037D VAL 6.0 1.1 - - - +
1330D ASN* 5.7 1.3 - - - +
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Residues in contact with TYR 103 (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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74D THR* 3.9 17.9 + - - +
77D LEU* 4.9 7.0 - - + -
100D ASP* 3.0 20.1 + - + +
102D ILE* 1.3 77.0 - - - +
104D ALA* 1.3 66.7 + - - +
106D LYS* 3.0 15.3 + - + +
107D LEU* 3.0 53.8 + - + +
262D ILE* 4.9 2.1 - - - +
263D LEU 4.7 0.9 + - - -
264D TYR* 4.2 4.3 - - - -
265D GLY* 3.4 36.6 + - - -
502D ADP 3.3 72.5 + + - +
1330D ASN* 6.2 0.7 - - - -
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Residues in contact with ALA 104 (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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77D LEU* 4.2 34.3 - - + +
99D LEU* 4.5 3.1 - - + -
100D ASP 2.9 12.2 + - - +
101D PRO* 3.4 11.9 - - + +
103D TYR* 1.3 77.5 - - - +
105D ARG* 1.3 60.4 + - - +
107D LEU* 3.2 9.0 + - - +
108D GLY 3.4 0.2 + - - -
109D VAL* 3.0 26.9 + - + +
111D ILE* 3.6 16.4 - - + -
1029D LEU* 4.4 7.0 - - + -
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Residues in contact with ARG 105 (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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101D PRO 2.9 8.8 + - - +
102D ILE* 3.5 32.1 + - - +
103D TYR 3.2 0.2 - - - -
104D ALA* 1.3 76.8 - - - +
106D LYS* 1.3 59.3 + - - +
108D GLY* 2.8 21.5 + - - -
109D VAL 3.7 14.0 + - - +
111D ILE* 3.5 28.7 - - + +
112D ASP* 5.9 1.0 + - - -
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Residues in contact with LYS 106 (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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102D ILE* 3.1 31.6 + - - +
103D TYR* 3.0 22.1 + - + +
105D ARG* 1.3 78.1 - - - +
107D LEU* 1.3 58.0 + - - +
108D GLY* 3.3 3.5 + - - -
265D GLY* 3.6 38.3 - - - +
266D GLU* 4.0 6.1 - - - +
1329D SER 5.3 1.8 + - - -
1330D ASN* 3.3 28.6 - - - +
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Residues in contact with LEU 107 (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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74D THR* 3.9 21.3 - - + +
77D LEU* 3.8 31.9 - - + -
78D GLN* 3.0 25.0 + - - +
81D ALA* 3.9 6.3 - - - +
85D ARG* 5.5 0.9 + - - -
103D TYR* 3.0 52.5 + - + +
104D ALA* 3.6 7.4 - - - +
105D ARG 3.1 0.8 - - - -
106D LYS* 1.3 76.3 - - - +
108D GLY* 1.3 59.9 + - - +
109D VAL* 3.5 1.8 - - + -
266D GLU 3.7 10.6 - - - +
267D 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