Contacts of the helix formed by residues 120 - 125 (chain J) in PDB entry 3MQT
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 PRO 120 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118J GLY 4.6 1.1 - - - +
119J VAL* 1.4 92.1 - - + +
121J ALA* 1.3 66.7 + - - +
122J TYR* 3.2 43.1 - - + +
123J LYS* 3.1 35.9 + - + +
124J LEU 4.0 1.2 + - - -
322J HIS* 3.8 4.0 - - + -
364J SER 3.8 4.0 - - - +
365J ASP* 3.6 20.4 - - + +
366J LYS 3.4 22.8 - - - +
368J GLY 3.6 0.7 - - - +
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Residues in contact with ALA 121 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J TYR* 4.1 18.4 - - + +
119J VAL 4.6 0.7 - - - -
120J PRO* 1.3 72.0 - - - +
122J TYR* 1.3 63.4 + - - +
124J LEU* 2.9 22.5 + - - +
125J MET* 3.0 24.1 + - + +
322J HIS* 3.4 3.7 + - - +
368J GLY* 2.8 25.3 + - - +
369J LEU* 3.6 26.7 - - + -
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Residues in contact with TYR 122 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J PRO* 3.4 26.5 - - + +
121J ALA* 1.3 77.0 - - - +
123J LYS* 1.3 75.1 + - + +
125J MET* 3.3 10.1 + - - -
126J GLY 3.5 0.9 + - - -
127J GLY* 2.9 21.7 + - - -
128J ALA* 3.9 26.0 - - + -
322J HIS* 3.0 38.2 + + - +
325J ILE* 3.5 24.9 - - + -
326J VAL* 3.5 10.1 - - + +
363J VAL* 4.1 15.8 + - + -
364J SER 3.5 13.6 - - - -
365J ASP* 4.2 11.6 + - - +
77L GLU* 3.9 16.4 - - - -
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Residues in contact with LYS 123 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119J VAL* 4.0 14.1 - - + -
120J PRO* 3.1 39.2 + - + +
121J ALA 3.1 0.2 + - - -
122J TYR* 1.3 93.6 + - + +
124J LEU* 1.3 60.4 + - - +
126J GLY 3.3 10.2 + - - -
127J GLY* 3.7 8.3 + - - +
365J ASP* 6.1 1.1 - - - -
74L ASP* 3.1 32.8 + - - +
76L LEU* 3.8 34.3 - - + +
77L GLU* 3.1 31.8 + - + +
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Residues in contact with LEU 124 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76J LEU* 4.1 21.8 - - + -
78J PHE* 3.8 23.1 - - + -
110J TYR* 4.2 16.6 - - + +
113J ALA* 3.7 17.3 - - + +
114J GLY* 3.6 34.8 - - - +
117J LEU* 4.1 10.5 - - + -
119J VAL* 4.2 8.3 - - + -
120J PRO 4.6 1.1 - - - +
121J ALA* 2.9 11.2 + - - +
123J LYS* 1.3 74.7 - - - +
125J MET* 1.3 58.8 + - - +
126J GLY 3.2 3.6 + - - -
293J LEU* 5.3 1.4 - - - +
76L LEU* 3.9 27.4 - - + -
124L LEU* 6.0 0.2 - - + -
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Residues in contact with MET 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110J TYR* 4.1 12.8 - - + -
121J ALA* 3.0 28.1 + - + +
122J TYR* 3.7 7.4 - - - +
123J LYS 3.2 0.8 - - - -
124J LEU* 1.3 77.1 - - - +
126J GLY* 1.3 56.1 + - - +
127J GLY 3.6 1.8 - - - -
289J VAL* 3.8 40.4 - - + -
293J LEU* 4.0 21.4 - - + +
319J ALA 4.7 1.6 - - - +
322J HIS* 3.8 25.8 - - + +
323J PHE* 3.5 32.3 - - - +
326J VAL* 3.4 26.3 - - + +
369J LEU* 4.3 8.3 - - + -
79L ARG* 3.8 9.7 - - - -
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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