Contacts of the helix formed by residues 94 - 99 (chain A) in PDB entry 2JAJ
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 ALA 94 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LEU* 3.7 30.1 - - + -
92A PRO* 3.3 7.5 - - - +
93A GLY* 1.3 76.1 - - - +
95A PRO* 1.3 70.9 - - + +
96A SER* 4.4 3.8 - - - +
97A ARG* 3.0 30.1 + - + +
98A ARG* 3.9 2.3 + - - +
126A ASP* 4.7 0.6 + - - -
144A ARG* 3.7 21.3 - - - +
500A D20 6.1 0.2 - - - +
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Residues in contact with PRO 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLY 3.4 6.5 - - - +
94A ALA* 1.3 83.7 - - + +
96A SER* 1.3 62.9 + - - +
97A ARG 3.1 1.7 + - - -
98A ARG* 3.2 50.8 + - - +
144A ARG* 5.2 1.8 - - - +
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Residues in contact with SER 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.4 15.1 - - - +
69A SER 5.4 0.7 - - - +
70A LEU* 3.9 17.5 - - - +
71A PRO* 6.0 1.7 - - - +
94A ALA* 3.1 6.6 - - - +
95A PRO* 1.3 80.6 - - - +
97A ARG* 1.3 67.4 + - - +
98A ARG 3.4 0.6 + - - -
99A LYS* 4.7 1.8 + - - +
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Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A LEU* 4.5 7.0 - - + -
72A ASP* 3.5 32.9 + - + +
75A PHE* 3.0 24.7 + - - +
78A ASP* 2.8 35.9 + - - +
79A VAL* 4.2 3.3 - - - +
92A PRO* 4.0 18.7 - - + +
94A ALA* 3.0 28.3 + - + +
96A SER* 1.3 84.0 - - - +
98A ARG* 1.3 64.0 + - - +
99A LYS 3.3 2.0 - - - -
100A GLU* 2.7 64.9 + - - +
126A ASP* 4.6 6.6 + - - -
500A D20 3.5 19.1 + - - +
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Residues in contact with ARG 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ARG* 3.3 47.4 - - + +
92A PRO* 2.7 44.2 + - + +
93A GLY 3.5 12.9 + - - -
94A ALA 4.0 2.5 - - - +
95A PRO* 3.2 41.2 + - - +
96A SER 3.4 0.4 - - - -
97A ARG* 1.3 76.7 - - - +
99A LYS* 1.3 63.5 + - + +
100A GLU 3.2 1.4 + - - -
101A VAL* 3.2 27.5 + - - +
124A THR* 3.4 23.0 - - - +
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Residues in contact with LYS 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ARG* 5.4 0.3 + - - -
70A LEU* 4.0 24.2 - - + +
96A SER 4.7 1.4 + - - +
97A ARG 3.3 0.8 - - - -
98A ARG* 1.3 74.2 - - + +
100A GLU* 1.3 63.9 + - - +
101A VAL 3.1 3.2 + - - -
102A ASP* 3.3 37.8 + - - +
103A MET 4.7 0.5 + - - -
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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