Contacts of the strand formed by residues 97 - 101 (chain C) in PDB entry 2JIX
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 GLU 97 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57C TYR* 3.6 0.5 - - - -
58C GLN* 3.1 38.2 + - + +
60C GLU* 5.8 0.9 - - - +
64C TRP* 3.8 25.0 - - + -
96C LEU* 1.3 77.0 - - - +
98C LEU* 1.3 60.6 + - - +
99C ARG* 4.3 1.4 + - - -
110C HIS* 2.8 31.3 + - - +
111C ARG 3.2 10.3 - - - +
112C VAL* 3.9 12.8 - - + -
99F ARG* 3.2 13.8 + - - +
100F LEU* 2.8 43.5 + - + +
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Residues in contact with LEU 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C LEU* 3.4 26.7 - - + -
28C CYS* 3.6 26.2 - - - -
36C LEU* 5.2 0.4 - - + -
38C CYS* 4.0 6.1 - - - -
55C PHE* 3.6 22.2 - - + -
56C SER 3.2 11.9 - - - +
57C TYR* 4.1 6.7 - - + -
64C TRP* 4.3 1.3 - - - -
67C CYS* 4.8 0.7 - - - -
96C LEU* 3.7 13.7 - - + -
97C GLU* 1.3 75.5 - - - +
99C ARG* 1.3 60.6 + - - +
100C VAL* 3.9 8.5 - - + -
109C TYR* 4.9 2.2 - - + -
110C HIS* 3.3 6.4 - - - -
111C ARG* 2.9 41.1 + - + +
113C ILE* 3.7 21.1 - - + -
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Residues in contact with ARG 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 3.3 24.9 + - - -
54C SER 3.8 1.4 - - - +
56C SER* 2.5 46.1 + - - +
64C TRP* 3.7 20.4 - - + -
97C GLU* 4.3 2.2 + - - -
98C LEU* 1.3 73.6 - - - +
100C VAL* 1.3 58.8 + - - +
101C THR* 4.1 9.7 + - + +
107C PRO* 5.8 2.7 - - + -
109C TYR 3.5 2.7 - - - +
110C HIS* 3.4 43.7 + - + -
33F TYR* 3.2 60.6 - - - +
50F TYR* 4.3 19.6 - - - -
98F GLU* 3.7 24.5 + - - +
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Residues in contact with VAL 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C TRP* 3.9 27.4 - - + -
53C TYR* 5.2 0.4 - - + -
54C SER 3.4 9.0 - - - +
55C PHE* 3.6 45.5 - - + -
98C LEU* 3.9 9.0 - - + -
99C ARG* 1.3 76.1 - - - +
101C THR* 1.3 60.3 + - - +
107C PRO 3.7 0.3 - - - -
108C ARG* 2.7 38.2 + - + +
109C TYR* 2.7 39.4 + - + +
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Residues in contact with THR 101 (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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53C TYR* 3.4 8.4 - - - +
54C SER* 2.7 53.9 + - - -
99C ARG* 4.9 10.5 - - + +
100C VAL* 1.3 81.4 - - - +
102C ALA* 1.3 59.5 + - - +
105C GLY* 3.7 19.9 - - - -
106C ALA 3.4 8.5 - - - -
107C PRO* 3.8 17.0 - - + -
108C ARG* 5.0 0.7 - - - -
50F TYR* 3.9 17.5 - - - +
54F GLU* 6.0 1.6 - - - +
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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
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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