Contacts of the helix formed by residues 119 - 123 (chain C) in PDB entry 1JT7
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 ARG 119 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C ASP* 2.8 46.4 + - - +
71C GLY 3.5 10.1 - - - +
72C LEU* 3.8 15.5 - - + -
117C CYS 4.0 0.8 + - - -
118C LYS* 1.3 74.1 - - - +
120C GLY* 1.3 57.9 + - - +
121C PRO* 3.3 20.4 - - + +
122C ARG* 2.8 60.8 + - + +
123C THR* 3.6 4.0 + - - +
68D ASP* 3.0 42.5 + - + +
69D THR* 4.0 5.3 + - - +
74D TYR* 3.5 55.7 - - - +
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Residues in contact with GLY 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67C MET* 4.0 10.5 - - - +
71C GLY 2.8 18.1 + - - -
107C TRP* 3.4 31.6 - - - -
118C LYS 3.8 1.4 + - - -
119C ARG* 1.3 68.7 - - - +
121C PRO* 1.3 65.8 - - - +
123C THR* 2.7 32.7 + - - +
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Residues in contact with PRO 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C GLY* 4.2 1.3 - - - -
107C TRP* 3.3 41.3 - - + +
119C ARG* 3.6 33.4 - - + +
120C GLY* 1.3 89.8 - - - +
122C ARG* 1.3 83.5 + - - +
123C THR 3.2 7.4 + - - +
124C HIS* 5.3 1.2 + - - -
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Residues in contact with ARG 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118C LYS* 3.1 8.2 + - - -
119C ARG* 2.8 43.7 + - + +
121C PRO* 1.3 97.2 + - - +
123C THR* 1.3 59.3 + - - +
124C HIS* 3.9 5.8 + - - -
127C GLN* 2.9 21.1 + - - -
68D ASP* 3.0 37.7 + - - +
70D ASP* 3.5 39.7 - - - +
72D LEU* 3.8 28.5 - - - +
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Residues in contact with THR 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ASN* 3.6 8.0 + - - +
107C TRP* 5.6 0.2 - - - -
108C PHE* 2.9 50.4 + - + +
110C GLY 4.7 3.1 - - - +
118C LYS* 3.7 33.9 - - + -
119C ARG 3.8 7.4 - - - +
120C GLY 2.7 19.1 + - - +
121C PRO* 3.8 6.6 - - - +
122C ARG* 1.3 83.2 - - - +
124C HIS* 1.3 67.5 + - - +
127C GLN* 3.1 7.6 - - - +
130C ILE* 4.2 4.5 - - + -
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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