Contacts of the helix formed by residues 123 - 129 (chain H) in PDB entry 2ZJP
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 PHE 123 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29H ILE* 3.3 46.0 - - + -
48H GLY 4.0 6.1 - - - -
50H ILE* 3.7 21.3 - - + -
73H VAL* 3.4 36.3 - - + -
99H ILE* 4.6 1.8 - - + -
103H GLY* 3.7 26.5 - - - +
118H LEU* 3.0 19.0 + - + +
121H ARG* 3.5 27.6 - - + -
122H ARG* 1.3 73.5 - - - +
124H MET* 1.3 65.1 + - - +
125H LYS* 2.8 5.2 + - - -
126H ILE* 2.9 32.3 + - + -
127H VAL* 3.3 10.0 - - - +
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Residues in contact with MET 124 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118H LEU 4.6 0.2 + - - -
119H ARG* 4.6 29.2 - - + +
122H ARG* 2.7 51.2 + - + +
123H PHE* 1.3 68.8 - - - +
125H LYS* 1.3 59.5 + - + +
127H VAL* 3.0 14.7 - - - +
128H SER* 2.7 31.1 + - - +
44M ARG* 6.4 0.2 - - - +
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Residues in contact with LYS 125 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H GLY 5.3 1.3 - - - +
104H GLU* 3.2 42.1 + - + +
105H PRO* 4.4 14.8 - - + -
123H PHE 2.8 4.7 + - - +
124H MET* 1.3 73.6 - - + +
126H ILE* 1.3 67.6 + - + +
128H SER* 2.7 29.0 + - - +
129H LEU* 3.3 10.3 + - + +
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Residues in contact with ILE 126 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73H VAL* 3.8 9.6 - - + -
75H VAL* 4.1 1.8 - - + -
97H VAL* 3.2 49.6 - - + -
99H ILE* 4.0 8.3 - - + -
103H GLY 4.0 6.3 - - - +
105H PRO* 3.9 19.3 - - + +
110H VAL* 3.4 24.8 - - + +
114H VAL* 5.3 1.9 - - + +
118H LEU* 3.6 25.4 - - + -
123H PHE* 2.9 40.0 + - + +
125H LYS* 1.3 74.8 - - - +
127H VAL* 1.3 61.4 + - - +
129H LEU 3.5 1.9 + - - -
130H ALA* 3.7 4.2 + - - +
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Residues in contact with VAL 127 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114H VAL* 4.6 5.2 - - + -
118H LEU* 4.4 25.6 - - + +
119H ARG* 3.8 25.8 - - + +
123H PHE 3.3 13.5 - - - +
124H MET* 3.0 18.6 - - - +
126H ILE* 1.3 69.2 - - - +
128H SER* 1.3 59.6 + - - +
129H LEU 3.0 2.7 - - - -
130H ALA* 2.5 37.5 + - + +
133H VAL* 3.4 36.9 - - + +
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Residues in contact with SER 128 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H MET* 2.7 19.8 + - - +
125H LYS* 2.7 22.7 + - - +
127H VAL* 1.3 76.4 - - - +
129H LEU* 1.3 66.2 + - - +
130H ALA 3.6 1.2 + - - +
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Residues in contact with LEU 129 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105H PRO* 3.7 29.8 - - + -
107H GLY 4.8 0.4 - - - +
108H THR 4.0 12.6 - - - +
109H ARG* 3.7 25.6 - - + +
110H VAL* 3.6 32.2 + - + +
125H LYS 3.3 9.1 + - - +
126H ILE 3.5 1.3 + - - -
127H VAL 3.0 1.0 - - - -
128H SER* 1.3 83.7 - - - +
130H ALA* 1.3 59.5 + - - +
131H PRO* 3.1 15.2 - - - +
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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