Contacts of the helix formed by residues 128 - 136 (chain G) in PDB entry 1CJ1
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 LEU 128 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G TRP* 4.3 13.7 - - + -
61G PHE* 4.9 2.2 - - + -
85G ILE* 4.6 15.3 - - + -
95G PHE* 3.9 43.7 - - + -
110G VAL* 4.4 12.6 - - + -
118G TYR* 3.5 34.5 - - + -
127G SER* 1.3 70.7 - - - +
129G ASN* 1.3 64.6 - - - +
131G LEU* 3.7 8.2 - - + +
132G VAL* 2.7 30.1 + - + +
61H PHE* 4.9 8.5 - - + -
87H GLU* 3.0 15.3 + - - +
95H PHE* 4.5 7.9 - - + -
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Residues in contact with ASN 129 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58G HIS* 3.1 28.2 + - - -
60G TRP* 3.9 14.5 - - - -
127G SER* 3.5 5.8 - - - +
128G LEU* 1.3 75.9 - - - +
130G GLU* 1.3 64.5 + - + +
132G VAL* 3.5 1.2 - - - +
133G ASP* 2.9 40.9 + - - -
63H GLY* 4.2 1.6 - - - -
64H LYS* 2.8 36.0 + - + +
65H ILE* 5.7 0.2 - - - +
87H GLU* 2.6 21.7 + - - +
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Residues in contact with GLU 130 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125G PHE* 4.0 14.1 - - + -
126G ASN* 3.3 23.0 + - - -
127G SER* 2.5 40.8 + - - +
129G ASN* 1.3 75.4 - - + +
131G LEU* 1.3 68.5 + - - +
132G VAL 3.0 0.2 + - - -
133G ASP* 3.1 6.7 + - - +
134G TYR* 2.8 25.1 + - - +
64H LYS* 3.6 26.6 + - + -
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Residues in contact with LEU 131 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85G ILE* 5.7 3.4 - - + -
97G LEU* 5.1 9.2 - - + -
110G VAL* 4.2 14.8 - - + -
118G TYR* 4.1 10.3 - - + -
119G PHE* 3.8 38.1 - - - +
120G LEU* 4.2 15.9 - - + -
125G PHE* 3.6 30.3 - - + -
127G SER 2.8 14.1 + - - +
128G LEU* 3.7 9.9 - - + +
130G GLU* 1.3 79.4 - - - +
132G VAL* 1.3 75.0 + - + +
134G TYR* 3.5 0.2 - - - +
135G HIS* 3.1 39.5 + - + +
148G LEU* 5.6 0.4 - - + -
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Residues in contact with VAL 132 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60G TRP* 4.1 33.2 - - + +
83G PHE* 3.6 39.3 - - + -
85G ILE* 4.2 14.8 - - + -
97G LEU* 5.9 1.1 - - + -
128G LEU 2.7 24.2 + - - +
129G ASN 3.5 2.9 - - - +
131G LEU* 1.3 81.6 - - + +
133G ASP* 1.3 71.4 + - - +
135G HIS 3.2 6.2 + - - -
136G ARG* 3.4 12.3 + - - +
148G LEU* 3.3 17.3 - - + +
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Residues in contact with ASP 133 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58G HIS* 6.1 0.2 - - - -
60G TRP* 5.2 1.2 + - - -
129G ASN* 2.9 34.1 + - - +
130G GLU* 3.8 4.8 - - - +
132G VAL* 1.3 79.1 - - - +
134G TYR* 1.3 56.9 + - - +
136G ARG* 2.6 62.8 + - - +
137G SER* 3.9 1.6 + - - -
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Residues in contact with TYR 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123G VAL* 4.0 24.2 - - + +
125G PHE* 3.5 28.7 - + + -
130G GLU 2.8 16.6 + - - +
131G LEU 3.5 3.1 - - - +
133G ASP* 1.3 79.6 - - - +
135G HIS* 1.3 86.0 + + - +
136G ARG 3.1 0.7 + - - -
137G SER* 3.1 24.4 + - - -
138G THR* 3.4 41.4 + - + +
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Residues in contact with HIS 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120G LEU* 4.2 22.8 - - + +
121G TRP* 5.1 6.5 - + - -
125G PHE* 4.2 11.5 - + - -
131G LEU* 3.1 35.1 + - + -
132G VAL 3.2 1.6 + - - -
133G ASP 3.1 1.0 - - - -
134G TYR* 1.3 101.9 - + - +
136G ARG* 1.3 65.5 + - - +
137G SER 2.8 1.6 - - - -
138G THR* 2.9 27.9 + - + +
139G SER 4.0 8.5 - - - -
140G VAL* 3.4 19.3 - - + +
146G ILE 4.6 0.3 - - - +
147G PHE* 3.7 3.6 - - - -
148G LEU* 3.0 39.4 + - + +
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Residues in contact with ARG 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G TRP* 4.0 19.4 - - - +
83G PHE* 4.7 1.7 - - - -
132G VAL* 3.4 11.5 + - - +
133G ASP* 2.6 45.2 + - - +
135G HIS* 1.3 83.6 - - - +
137G SER* 1.3 59.6 + - - +
147G PHE* 3.4 17.8 - - - +
148G LEU* 3.4 25.2 + - + +
149G ARG* 4.5 1.2 - - - +
150G ASP* 3.0 47.6 + - - +
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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
------------------------------------------------------------
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