Contacts of the strand formed by residues 94 - 104 (chain H) in PDB entry 1J5O
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 ILE 94 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41H GLN* 3.0 28.1 + - + +
93H ALA* 1.3 77.3 - - - +
95H TYR* 1.3 60.1 + - - +
96H TYR* 2.8 46.6 - - + +
116H GLY* 3.3 6.5 - - - +
117H THR 3.0 27.1 - - - +
118H SER* 3.6 23.6 - - - +
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Residues in contact with TYR 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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6H GLU* 3.6 4.7 - - - +
18H PHE* 3.2 34.3 - + - -
20H LEU* 3.7 24.2 - - + -
38H TRP* 5.0 7.2 - + + -
39H ILE 3.1 8.5 - - - +
40H ARG* 3.2 28.0 - - + +
50H LEU* 3.9 12.8 - - + -
82H LEU* 5.0 3.1 - - + -
84H MET* 4.0 7.6 - - + -
91H ASP* 2.3 36.0 + - - +
93H ALA* 2.8 28.9 - - - -
94H ILE* 1.3 69.6 - - - +
96H TYR* 1.3 64.1 + - - +
116H GLY* 3.1 1.4 - - - -
117H THR* 2.6 37.8 + - - +
119H VAL* 3.4 17.4 - - + +
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Residues in contact with TYR 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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6H GLU* 4.4 2.9 - - - -
38H TRP* 3.3 12.4 - - - -
39H ILE* 2.7 43.0 + - + +
41H GLN* 3.6 28.7 + - + +
47H LEU* 6.1 1.8 - - + -
94H ILE* 2.8 47.1 - - + +
95H TYR* 1.3 76.6 - - - +
97H CYS* 1.3 60.9 + - - +
98H ALA 4.2 0.2 - - - -
113H TRP* 4.0 31.9 - + + -
114H GLY 4.0 10.8 - - - +
115H GLN* 4.3 4.3 - - - -
116H GLY* 3.3 25.9 + - - -
38L GLN* 4.6 0.2 - - - -
42L GLY* 3.8 26.8 + - - -
44L VAL* 4.4 11.4 - - + -
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Residues in contact with CYS 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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4H LEU* 3.6 17.3 - - - +
6H GLU* 3.3 26.9 - - - +
22H CYS* 2.0 55.2 - - + -
36H VAL* 5.8 1.8 - - + -
37H THR 3.0 9.0 - - - +
38H TRP* 3.5 16.6 - - + -
96H TYR* 1.3 76.0 - - - +
98H ALA* 1.3 61.1 + - - +
113H TRP 4.1 9.9 - - - -
114H GLY* 4.4 0.9 + - - -
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Residues in contact with ALA 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4H LEU* 4.3 3.4 - - - -
36H VAL* 3.3 2.8 - - - -
37H THR* 2.7 45.0 + - - +
39H ILE* 4.9 4.0 - - + +
96H TYR 4.2 0.6 - - - -
97H CYS* 1.3 75.6 - - - +
99H GLN* 1.3 63.8 + - - +
100H SER 3.2 1.4 + - - -
110H MET* 4.2 12.3 - - + -
112H HIS 3.2 13.9 - - - +
113H TRP* 3.8 34.3 - - + +
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Residues in contact with GLN 99 (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 ILE* 4.4 12.1 - - + +
4H LEU* 3.9 9.2 - - + +
27H PHE* 3.7 53.4 - - + +
34H ILE* 4.5 6.0 - - + +
35H GLY 3.6 6.5 - - - +
36H VAL* 4.7 0.9 - - - +
98H ALA* 1.3 69.4 - - - +
100H SER* 1.3 64.2 + - - +
101H ALA* 3.8 17.4 - - - +
110H MET* 3.5 2.9 - - - -
111H ASP* 3.4 39.8 + - - +
112H HIS* 2.8 30.2 + - + +
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Residues in contact with SER 100 (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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33H GLY 4.3 0.2 - - - -
34H ILE* 3.4 0.7 - - - -
35H GLY* 2.9 44.7 + - - +
36H VAL 3.6 0.5 + - - -
37H THR* 2.6 28.6 + - - -
52H THR* 3.7 10.0 - - - +
54H TRP* 5.3 6.5 - - - -
98H ALA 3.2 0.4 + - - -
99H GLN* 1.3 75.7 - - - +
101H ALA* 1.3 64.6 + - - +
108H SER* 5.5 1.6 - - - -
109H ALA 3.3 10.8 - - - -
110H MET* 4.3 8.1 - - - +
96L TRP* 5.0 11.7 - - - -
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Residues in contact with ALA 101 (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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33H GLY 2.9 13.5 - - - +
34H ILE* 4.3 9.2 - - + -
54H TRP* 5.7 0.4 - - - -
99H GLN* 3.8 20.2 - - - +
100H SER* 1.3 78.2 - - - +
102H ILE* 1.3 63.1 + - - +
103H THR* 3.1 12.3 + - - +
108H SER* 3.9 5.2 + - - -
109H ALA 3.1 27.4 + - - +
111H ASP* 4.1 6.6 + - - +
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Residues in contact with ILE 102 (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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223B LYS 4.3 3.8 - - - +
224B GLU* 3.1 19.7 - - - +
227B PHE* 3.2 20.9 - - + -
229B TRP* 4.0 16.6 - - + -
230B MET* 3.6 37.9 - - + +
33H GLY* 2.7 23.9 + - - +
54H TRP* 3.2 22.9 - - + -
55H TRP* 6.1 0.7 - - - +
101H ALA* 1.3 70.9 - - - +
103H THR* 1.3 64.0 + - - +
104H SER 3.9 5.4 - - - +
107H ASP 3.4 8.7 - - - +
108H SER* 2.9 24.0 - - - +
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Residues in contact with THR 103 (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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230B MET* 3.1 10.2 - - - +
101H ALA* 3.1 12.7 + - - +
102H ILE* 1.3 75.0 - - - +
104H SER* 1.3 64.3 + - - +
107H ASP* 2.8 30.5 + - + +
108H SER* 4.3 1.4 + - - -
109H ALA* 4.5 4.5 + - - +
111H ASP* 4.5 10.6 + - - -
49L TYR* 4.8 14.0 - - + +
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Residues in contact with SER 104 (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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227B PHE* 3.6 7.3 - - - -
230B MET* 3.2 18.0 - - - +
102H ILE* 3.9 2.6 - - - +
103H THR* 1.3 86.2 - - - +
105H VAL* 1.3 74.9 + - - +
106H THR* 2.6 19.1 + - - -
107H ASP* 2.8 30.9 + - - +
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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