Contacts of the strand formed by residues 95 - 105 (chain A) in PDB entry 5HRI
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 LYS 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ILE 3.5 0.5 - - - +
91A GLU* 3.5 4.9 - - - -
92A TRP* 2.8 37.2 + - - +
93A GLU 3.0 9.5 + - - +
94A LYS* 1.3 85.0 - - + +
96A THR* 1.3 63.0 + - - +
97A TYR* 3.8 28.1 - - + +
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Residues in contact with THR 96 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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0A GLY* 4.3 12.5 + - - -
89A PHE* 4.0 31.6 - - + -
90A ILE 3.3 4.9 - - - +
91A GLU* 2.4 32.0 + - - +
95A LYS* 1.3 73.8 - - - +
97A TYR* 1.3 73.4 + - - +
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Residues in contact with TYR 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0A GLY* 3.3 26.9 - - - +
1A MET 3.9 6.6 + - - -
2A LEU* 3.9 29.2 - - + -
6A GLN* 4.0 19.4 + - + -
10A ILE* 4.3 12.6 - - + -
50A VAL* 6.0 1.8 - - + -
89A PHE* 3.4 7.6 - - - -
90A ILE* 2.9 43.5 + - + +
92A TRP* 3.8 47.8 - + + -
95A LYS* 3.8 22.9 - - + +
96A THR* 1.3 79.1 - - - +
98A GLN* 1.3 64.2 + - - +
15F T 5.8 0.2 + - - -
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Residues in contact with GLN 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0A GLY 5.2 6.8 + - - +
48A ASN 4.6 5.6 + - - +
49A ASP* 3.2 22.7 + - + +
50A VAL* 3.0 26.2 + - - +
79A LYS* 4.3 8.1 + - - -
87A VAL* 3.7 20.9 - - + +
88A LEU 3.5 5.2 - - - +
89A PHE* 3.6 25.6 - - + -
97A TYR* 1.3 75.6 - - - +
99A LEU* 1.3 59.9 + - - +
100A ASP* 3.1 29.7 + - - +
9D A 3.3 25.9 + - - -
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Residues in contact with LEU 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ILE* 5.5 0.7 - - + -
14A LEU* 3.9 27.8 - - + -
18A LEU* 5.7 1.1 - - + -
50A VAL* 3.4 33.4 - - + +
52A LEU* 4.1 6.5 - - + -
71A ILE* 4.3 9.2 - - + -
86A CYS 3.9 0.9 - - - +
87A VAL* 3.6 0.2 - - - -
88A LEU* 2.8 55.8 + - + +
90A ILE* 4.1 31.9 - - + -
97A TYR 3.7 1.0 + - - -
98A GLN* 1.3 72.6 - - - +
100A ASP* 1.3 63.6 + - - +
101A LEU* 3.7 28.5 - - + -
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Residues in contact with ASP 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASP* 3.3 9.2 - - - +
50A VAL 2.7 11.3 + - - +
51A ASP* 3.1 14.4 - - - +
52A LEU 2.8 28.1 + - - +
86A CYS 3.5 4.5 - - - +
87A VAL* 3.6 14.1 - - + +
98A GLN* 3.1 25.5 + - - +
99A LEU* 1.3 76.3 - - - +
101A LEU* 1.3 64.6 + - - +
102A PHE* 3.6 16.8 - - + -
203A MN 2.0 35.7 + - - -
9D A 3.9 6.2 - - - +
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Residues in contact with LEU 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A LEU* 5.1 7.6 - - + -
52A LEU* 3.4 20.6 - - + +
54A ILE* 4.5 10.1 - - + -
66A LEU* 3.9 22.5 - - + +
69A ILE* 3.9 31.4 - - + -
85A LYS* 3.5 3.5 - - - -
86A CYS* 2.7 45.7 + - + +
88A LEU* 4.1 20.6 - - + -
99A LEU* 3.7 30.7 - - + -
100A ASP* 1.3 78.3 - - - +
102A PHE* 1.3 65.3 + - - +
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Residues in contact with PHE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A VAL* 4.7 2.5 - - + -
51A ASP* 3.7 16.8 - - + -
52A LEU 3.0 18.1 + - - -
53A LEU* 3.5 5.3 - - + +
54A ILE* 2.7 36.0 + - - +
66A LEU* 4.5 0.4 - - - -
84A ARG 3.2 13.7 - - - +
85A LYS* 3.9 24.7 - - + -
100A ASP* 3.6 32.5 - - + -
101A LEU* 1.3 77.3 - - - +
103A THR* 1.3 60.4 + - - +
116A PHE* 3.3 54.5 - + + -
201A DGT 5.3 0.2 - - - -
9D A 3.9 30.1 - - + -
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Residues in contact with THR 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 4.1 2.3 - - - +
54A ILE* 3.3 8.1 - - + +
56A VAL* 4.0 20.0 - - + -
62A LEU* 3.4 20.5 - - + +
65A VAL* 4.5 5.4 - - + -
66A LEU* 3.6 32.1 - - + -
83A GLU 2.7 21.9 + - - +
84A ARG* 2.9 32.4 + - - +
102A PHE* 1.3 78.1 - - - +
104A ALA* 1.3 62.5 + - - +
116A PHE* 5.3 3.8 - - - -
140A TYR* 5.3 1.0 - - - -
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Residues in contact with ALA 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A LEU* 3.8 9.4 - - + +
54A ILE 3.0 5.7 + - - -
55A ILE* 3.4 17.3 - - + -
56A VAL* 3.0 28.0 + - - +
84A ARG* 3.6 1.1 - - - +
103A THR* 1.3 75.6 - - - +
105A LEU* 1.3 66.0 + - - +
108A GLU* 3.4 12.8 - - + +
109A LYS* 4.7 1.3 - - - -
112A ALA* 3.6 31.2 - - + -
116A PHE* 6.0 0.2 - - + -
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Residues in contact with LEU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A ILE* 4.6 1.3 - - - -
56A VAL* 3.5 31.2 - - + +
57A PRO 5.4 0.2 - - - -
58A GLU* 4.1 1.1 - - - +
59A LYS* 4.0 42.0 - - + +
62A LEU* 4.2 8.1 - - + -
84A ARG* 4.3 11.4 - - - +
104A ALA* 1.3 73.8 - - - +
106A ALA* 1.3 58.1 + - - +
107A GLU* 3.1 25.4 - - - +
108A GLU* 2.6 57.2 + - - +
109A LYS* 3.2 8.0 + - - -
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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