Contacts of the helix formed by residues 102 - 106 (chain C) in PDB entry 1JPL
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 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55C GLN* 3.8 47.3 - - + +
95C LYS* 2.9 19.4 + - + +
96C VAL* 4.1 11.0 - - + -
101C TYR* 1.3 88.2 - - + +
103C GLY* 1.3 65.0 + - - +
104C ASP 3.3 3.1 - - - -
105C ARG* 2.9 28.3 + - + +
106C VAL* 3.1 25.1 - - + +
95D LYS* 5.3 10.8 - - - +
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Residues in contact with GLY 103 (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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95C LYS 3.6 3.4 + - - -
96C VAL 3.5 15.9 - - - -
97C VAL 4.4 2.0 - - - -
98C SER 2.8 25.9 + - - -
99C PRO* 4.0 4.0 - - - -
101C TYR 3.5 0.4 - - - -
102C LEU* 1.3 77.0 - - - +
104C ASP* 1.3 60.9 + - - +
105C ARG 3.2 1.2 + - - -
106C VAL* 3.3 4.3 + - - +
111C LYS* 3.0 28.8 + - - -
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Residues in contact with ASP 104 (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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99C PRO* 3.2 35.6 + - - +
101C TYR 4.9 0.2 + - - -
102C LEU 3.2 1.4 + - - -
103C GLY* 1.3 74.6 - - - +
105C ARG* 1.3 81.5 + - + +
106C VAL 3.6 2.0 + - - +
203D MSE 4.9 4.3 - - - +
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Residues in contact with ARG 105 (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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57C PRO* 5.1 6.1 - - - +
99C PRO 5.1 2.0 + - - -
101C TYR 3.6 22.7 + - - -
102C LEU* 2.9 19.4 + - + +
104C ASP* 1.3 103.3 + - + +
106C VAL* 1.3 63.2 + - + +
48D ARG* 4.1 21.1 + - - +
92D GLU* 5.3 6.3 + - - -
95D LYS* 6.1 1.2 - - - +
203D MSE 3.0 27.2 - - + +
307H GLU* 3.6 23.1 + - - -
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Residues in contact with VAL 106 (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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54C ILE 5.8 2.9 - - - +
55C GLN* 5.9 2.7 - - - +
56C SER 5.5 6.7 - - - +
57C PRO* 6.5 0.7 - - + -
96C VAL* 3.0 32.8 - - + +
102C LEU* 3.1 30.1 - - + +
103C GLY 3.3 11.6 - - - +
104C ASP 3.6 1.4 - - - +
105C ARG* 1.3 83.4 - - + +
107C SER* 1.3 59.8 + - - +
110C VAL* 5.0 11.4 - - + -
111C LYS* 2.8 42.2 + - + -
203D MSE 4.0 6.1 - - - +
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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