Contacts of the strand formed by residues 91 - 98 (chain H) 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 ALA 91 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38H ARG* 3.7 23.6 - - + -
39H GLN 3.0 23.3 - - - +
40H PRO* 3.4 8.7 - - + -
41H PRO* 4.2 5.4 - - - -
88H ALA 5.0 0.2 - - - +
89H ASP 3.4 4.2 + - - +
90H THR* 1.3 78.0 + - - +
92H VAL* 1.3 62.0 + - - +
93H TYR* 3.1 12.9 - - + -
111H LEU* 3.7 7.3 - - - +
112H VAL 3.1 27.9 + - - -
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Residues in contact with VAL 92 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38H ARG* 3.4 3.6 - - - -
39H GLN* 2.6 45.2 + - + +
41H PRO* 5.8 5.2 - - + -
91H ALA* 1.3 73.4 - - - +
93H TYR* 1.3 63.4 + - - +
94H TYR* 3.5 37.4 - - + +
109H GLY* 4.1 1.6 - - - -
110H THR 3.1 25.6 - - - +
111H LEU* 4.2 19.5 - - + +
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Residues in contact with TYR 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H GLU* 2.8 35.3 - - - +
18H LEU* 3.3 20.6 - - + +
20H LEU* 3.8 20.0 - - + -
36H TRP* 4.8 4.0 - + + -
37H ILE 3.9 2.2 - - - -
38H ARG* 3.1 36.1 + - + -
48H ILE* 3.9 11.0 - - + -
80H LEU* 3.9 21.8 - - + -
82H LEU* 3.4 18.9 - - + +
89H ASP 2.7 29.6 + - - -
91H ALA* 3.1 33.2 - - + -
92H VAL* 1.3 73.8 - - - +
94H TYR* 1.3 56.1 + - - +
110H THR 2.6 18.3 + - - +
112H VAL* 4.1 13.0 - - + -
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Residues in contact with TYR 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6H GLU* 3.9 2.5 - - - -
36H TRP* 3.3 8.6 - - - -
37H ILE* 2.9 44.4 + - + +
38H ARG 4.8 0.2 - - - -
39H GLN* 3.3 30.8 + - + -
45H LEU* 4.4 7.2 - - + -
92H VAL* 3.5 33.7 - - + +
93H TYR* 1.3 73.0 - - - +
95H CYS* 1.3 63.5 + - - +
106H TRP* 3.7 31.4 - + + -
107H GLY 3.5 12.8 - - - +
108H GLN 4.3 1.8 - - - -
109H GLY* 3.5 24.9 - - - -
38L GLN* 3.8 7.4 + - - -
42L LYS 4.5 5.7 + - - -
43L ALA* 4.0 22.9 - - + -
44L PRO* 4.2 5.6 - - + -
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Residues in contact with CYS 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 4.3 9.0 - - - +
6H GLU* 3.5 21.0 + - - -
22H CYS* 2.1 53.4 - - + -
35H SER 3.4 3.8 - - - -
36H TRP* 3.5 17.4 - - + -
78H PHE* 3.5 10.1 - - + -
94H TYR* 1.3 73.9 - - - +
96H ALA* 1.3 59.9 + - - +
106H TRP* 3.7 1.0 - - - -
107H GLY* 3.2 28.8 + - - +
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Residues in contact with ALA 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4H LEU* 4.9 1.6 - - - -
34H TRP* 3.1 11.2 - - - -
35H SER* 2.6 54.2 + - - +
37H ILE* 4.2 17.3 - - + -
78H PHE* 4.3 1.0 - - - -
95H CYS* 1.3 75.4 - - - +
97H ARG* 1.3 61.3 + - - +
103H GLY* 4.4 14.4 - - - -
105H TYR 3.4 11.2 - - - +
106H TRP* 4.3 10.8 - - + -
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Residues in contact with ARG 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2H VAL* 3.4 40.9 - - + +
4H LEU* 4.9 4.4 - - + +
27H ALA* 4.4 2.2 - - - +
32H TYR* 3.5 44.2 + - + -
33H TYR 4.1 4.9 - - - +
34H TRP* 3.4 30.8 - - + +
96H ALA* 1.3 71.6 - - - +
98H GLU* 1.3 68.6 + - - +
99H ARG* 3.8 17.3 - - - +
102H ILE 3.3 0.7 - - - +
104H ASP* 2.8 65.5 + - - +
105H TYR* 2.9 37.2 + - + +
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Residues in contact with GLU 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32H TYR* 4.3 4.2 - - - -
33H TYR* 2.8 49.0 + - + +
34H TRP 4.2 2.0 - - - +
35H SER* 2.9 29.7 + - - -
47H TRP* 3.1 31.4 + - - -
50H TYR* 4.6 6.1 - - + -
97H ARG* 1.3 74.5 - - - +
99H ARG* 1.3 63.0 + - - +
101H GLY 4.9 0.7 - - - +
102H ILE* 3.1 42.0 - - + +
103H GLY* 3.3 3.3 + - - -
94L TYR* 5.5 2.6 + - - +
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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