Contacts of the strand formed by residues 92 - 97 (chain C) in PDB entry 5JMO
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 92 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ARG* 3.8 12.6 - - + -
39C GLN 3.3 24.0 - - - +
40C ALA* 3.8 6.7 - - + +
41C PRO* 4.7 2.5 - - - -
90C ASP 3.2 5.4 + - - +
91C THR* 1.3 79.9 - - - +
93C LEU* 1.3 68.7 - - - +
94C TYR* 3.4 18.3 - - + -
112C GLN* 3.5 10.3 - - - +
113C VAL 3.2 26.4 + - - +
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Residues in contact with LEU 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38C ARG* 3.2 4.3 - - - -
39C GLN* 2.9 37.5 + - + +
92C ALA* 1.3 74.2 - - - +
94C TYR* 1.3 58.1 + - - +
95C TYR* 3.2 38.4 - - + +
109C GLN 4.2 6.1 - - - +
110C GLY* 3.7 4.9 - - - -
111C THR 3.3 36.3 - - - +
112C GLN* 3.5 16.6 + - - +
41D PRO* 5.8 3.4 - - + -
112D GLN* 3.5 41.3 - - + +
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Residues in contact with TYR 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLU* 3.9 6.2 - - - +
20C LEU* 3.9 26.9 - - + -
36C TRP* 4.6 8.1 - + + -
37C VAL 3.6 4.0 - - - -
38C ARG* 3.0 38.4 + - + -
48C VAL* 4.3 10.5 - - + -
68C PHE* 4.5 2.0 - + - -
81C LEU* 4.3 11.7 - - + -
83C MET* 3.3 27.3 - - + +
90C ASP* 2.7 30.9 + - - +
92C ALA* 3.4 20.9 - - + -
93C LEU* 1.3 74.1 - - - +
95C TYR* 1.3 61.1 + - - +
110C GLY* 3.3 3.9 - - - -
111C THR* 3.1 35.6 + - + +
113C VAL* 3.5 22.0 - - + -
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Residues in contact with TYR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C GLU* 3.3 3.8 - - - +
35C TYR 3.7 0.7 - - - +
36C TRP* 3.4 13.5 - - - -
37C VAL* 2.6 59.0 + - + +
39C GLN* 4.0 26.8 + - + +
45C LEU* 4.5 7.2 - - + -
93C LEU* 3.2 40.9 - - + +
94C TYR* 1.3 73.9 - - - +
96C CYS* 1.3 58.2 + - - +
107C ARG* 3.2 51.6 + - + -
108C GLY 3.2 9.2 - - - -
109C GLN 3.4 15.7 - - - -
110C GLY* 3.9 7.2 - - - -
41D PRO* 4.4 16.3 - - - +
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Residues in contact with CYS 96 (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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4C LEU* 3.6 8.2 - - + +
6C GLU* 2.6 21.8 + - + +
22C CYS* 2.0 50.0 - - + -
34C MET* 3.5 27.1 - - - -
35C TYR 3.6 3.8 - - - -
36C TRP* 4.2 5.6 - - + -
79C LEU* 4.0 6.5 - - - -
95C TYR* 1.3 73.5 - - - +
97C ALA* 1.3 61.9 + - - +
107C ARG* 3.5 1.0 - - - +
108C GLY 2.9 25.8 + - - -
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Residues in contact with ALA 97 (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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4C LEU* 4.0 2.2 - - - -
34C MET* 3.4 12.0 - - - +
35C TYR* 2.8 42.4 + - + +
37C VAL* 5.3 7.4 - - + -
96C CYS* 1.3 79.3 - - - +
98C VAL* 1.3 59.4 + - - +
99C GLY 3.2 23.1 - - - +
100C MET 5.6 0.2 - - - -
102C ALA* 4.4 0.4 - - + -
106C TRP 3.5 13.7 - - - +
107C ARG* 3.8 17.0 - - + -
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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