Contacts of the strand formed by residues 94 - 104 (chain B) in PDB entry 1HRN
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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0B THR* 5.3 2.7 - - - +
1B THR 5.4 0.2 - - - -
2B SER* 3.6 18.8 - - - -
89B ILE 3.6 0.3 - - - +
90B THR* 3.1 6.4 - - - +
91B VAL* 2.8 38.8 + - + +
93B GLY* 1.3 82.1 - - - +
95B THR* 1.3 74.4 + - - +
96B VAL* 4.3 2.0 - - + -
140B ILE* 3.8 36.6 - - + -
143B GLN* 3.8 14.8 - - - +
145B VAL* 4.3 8.7 - - + -
146B LEU* 3.4 32.5 - - + -
167B LEU* 5.1 4.5 - - + -
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Residues in contact with THR 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ILE* 4.0 15.6 - - + +
89B ILE 3.3 3.6 - - - -
90B THR* 3.8 20.8 + - - +
93B GLY 4.2 1.2 + - - -
94B ILE* 1.3 73.3 + - - +
96B VAL* 1.3 66.3 + - - +
143B GLN* 3.2 20.1 + - - +
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Residues in contact with VAL 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B ILE* 3.3 6.6 - - - +
89B ILE* 2.8 49.5 + - + +
91B VAL* 4.8 1.1 - - + -
94B ILE* 4.3 2.5 - - + -
95B THR* 1.3 79.9 - - - +
97B THR* 1.4 73.7 + - - +
99B GLN* 3.5 3.0 + - + +
136B ILE* 3.9 28.7 - - + -
139B ASN* 4.0 23.8 - - + +
140B ILE* 3.9 21.8 - - + -
143B GLN* 3.7 15.3 - - - +
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Residues in contact with THR 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B SER 5.7 1.3 - - - +
86B GLN* 2.8 35.7 - - - +
87B ASP* 3.3 16.8 - - - +
88B ILE* 4.1 15.7 - - + +
96B VAL* 1.4 80.4 - - - +
99B GLN* 1.3 61.5 + - - +
139B ASN* 3.9 12.5 + - - +
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Residues in contact with GLN 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B VAL* 4.2 12.5 + - + +
86B GLN* 4.3 4.9 - - - -
87B ASP 2.6 33.4 + - - +
89B ILE* 3.5 31.4 - - + -
96B VAL* 4.2 7.8 - - + +
97B THR* 1.3 77.6 - - - +
100B MET* 1.4 82.6 + - - +
101B PHE* 3.3 9.7 - - + -
133B VAL* 5.9 0.2 - - - +
134B THR 3.3 13.3 - - - +
135B PRO* 4.2 1.2 - - - +
136B ILE* 3.2 36.8 + - + +
139B ASN* 2.8 30.4 + - - +
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Residues in contact with MET 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B VAL* 4.7 3.3 + - - +
67B ASN* 4.2 16.6 - - - +
84B LEU* 3.5 27.4 - - + -
85B SER 3.3 17.3 - - - +
86B GLN* 3.7 23.4 - - + +
99B GLN* 1.4 95.2 - - - +
101B PHE* 1.3 59.3 + - - +
133B VAL* 3.6 27.1 - - + +
134B THR 5.4 2.9 + - - +
139B ASN* 5.0 2.0 + - - -
367B NAG 3.5 28.9 - - - +
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Residues in contact with PHE 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ILE* 3.8 14.8 - - + -
38B VAL* 3.6 29.4 - - + +
40B VAL* 4.1 20.0 - - + -
56B PHE* 3.5 38.1 - + - -
84B LEU* 3.4 9.7 - - - +
85B SER* 3.0 50.9 + - - +
87B ASP* 3.6 29.2 - - + -
89B ILE* 4.4 13.7 - - + -
99B GLN 3.3 13.9 - - - +
100B MET* 1.3 75.0 - - - +
102B GLY* 1.3 74.2 + - - +
103B GLU* 4.5 3.6 - - + -
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Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B VAL 2.9 15.7 + - - -
39B TRP* 3.4 7.6 - - - -
40B VAL 3.2 27.2 + - - +
71B LEU* 3.6 24.9 - - - -
73B LEU* 5.5 0.7 - - - -
83B PHE 3.9 0.2 - - - -
84B LEU* 4.4 0.2 - - - +
101B PHE* 1.3 81.1 - - - +
103B GLU* 1.3 61.5 + - - -
104B VAL* 3.6 2.2 + - - -
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Residues in contact with GLU 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL 3.9 2.2 - - - +
42B SER* 2.7 30.9 + - - +
43B SER* 2.9 19.8 + - - -
44B LYS* 4.4 4.7 - - - -
56B PHE* 3.8 29.2 - - + +
58B ALA* 4.6 4.0 - - - +
64B TYR* 4.4 5.9 - - - -
82B GLY* 2.8 11.2 - - - -
83B PHE* 2.8 65.3 + - + +
85B SER* 2.4 30.3 + - - +
101B PHE* 3.9 5.3 + - + -
102B GLY* 1.3 69.3 - - - -
104B VAL* 1.3 56.0 - - - +
105B THR 3.4 1.6 + - - -
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B TRP* 3.7 35.0 - - + -
40B VAL 2.9 17.9 + - - +
41B PRO* 3.7 2.7 - - + +
42B SER* 3.0 23.4 + - - +
45B CYS* 3.7 10.2 - - - -
50B CYS* 4.2 0.7 - - - -
71B LEU* 6.3 0.9 - - + -
73B LEU* 4.7 4.0 - - + -
80B VAL* 3.2 39.0 - - + -
81B SER 3.5 8.1 - - - +
82B GLY* 5.0 0.4 - - - -
102B GLY* 4.4 2.0 - - - +
103B GLU* 1.3 68.0 - - - +
105B THR* 1.3 56.8 + - - +
106B GLU 3.5 18.2 - - - +
107B MET* 3.8 15.9 - - + -
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Residues in contact with THR 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B SER* 3.7 5.4 - - - -
44B LYS* 3.4 18.8 + - - +
45B CYS* 3.5 20.6 - - - +
46B SER* 4.1 5.9 + - - -
47B TYR* 3.9 8.5 + - - -
81B SER* 3.0 5.1 + - - +
82B GLY* 3.8 18.6 - - - +
83B PHE* 3.2 27.3 - - + -
103B GLU 3.4 0.6 + - - -
104B VAL* 1.3 69.7 - - - +
106B GLU* 1.3 66.8 + - - +
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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