Contacts of the strand formed by residues 93 - 101 (chain A) in PDB entry 2HUE
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 THR 93 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A TYR* 3.4 40.4 - - + +
45A VAL* 2.6 33.7 + - - +
46A GLY 4.9 1.5 - - - -
48A SER 5.4 1.0 + - - -
88A GLU 5.7 3.4 - - - -
91A SER 4.5 1.3 - - - +
92A VAL* 1.3 79.8 - - - +
94A VAL* 1.3 76.6 + - - +
112A TYR* 3.5 2.8 - - - -
113A VAL* 2.8 37.6 + - + +
115A ASN* 4.2 4.0 - - - +
126B LEU* 3.8 12.9 - - - +
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Residues in contact with VAL 94 (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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45A VAL* 3.0 53.3 + - + +
93A THR* 1.3 85.0 + - - +
95A ILE* 1.3 69.4 + - - +
96A LEU* 4.7 4.5 - - + -
111A TYR 3.2 9.4 - - - +
112A TYR* 3.5 30.1 - - + -
113A VAL* 4.5 0.7 - - - +
126B LEU* 3.9 22.9 - - + +
129B ARG* 3.9 17.3 - - + -
130B ILE* 4.1 9.4 - - + -
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Residues in contact with ILE 95 (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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22A TYR* 4.2 13.2 - - + -
24A PHE* 3.6 32.1 - - + -
42A LEU* 4.5 9.0 - - + -
43A THR 3.3 9.2 - - - +
44A TYR* 3.5 33.0 - - + -
57A LEU* 5.5 1.8 - - + -
94A VAL* 1.3 75.3 - - - +
96A LEU* 1.3 63.7 + - - +
97A LEU* 6.0 0.2 - - + -
109A VAL 3.8 0.3 - - - +
110A GLY* 3.4 3.8 - - - -
111A TYR* 3.0 52.1 + - + -
113A VAL* 3.7 20.4 - - + +
139A ILE* 4.0 20.0 - - + -
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Residues in contact with LEU 96 (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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41A LYS 3.6 1.4 - - - +
42A LEU* 3.4 6.5 - - - +
43A THR* 2.8 51.4 + - + +
45A VAL* 3.8 18.4 - - + -
94A VAL* 4.7 2.9 - - + -
95A ILE* 1.3 83.4 - - - +
97A LEU* 1.3 60.3 + - - +
98A SER* 4.0 3.0 + - - +
108A ARG* 4.0 29.6 - - + +
109A VAL 3.3 2.9 - - - +
110A GLY* 4.0 12.8 - - - -
129B ARG* 3.2 61.2 - - + +
130B ILE* 4.4 1.6 - - - -
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Residues in contact with LEU 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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9A ILE* 3.8 22.7 - - + -
24A PHE* 3.7 37.9 - - + -
26A ILE* 4.0 13.7 - - + -
40A TRP* 5.4 6.0 - - + -
41A LYS 3.3 11.7 - - - +
42A LEU* 3.5 20.4 - - + -
74A PHE* 3.4 32.5 - - + -
95A ILE* 6.0 0.2 - - + -
96A LEU* 1.3 70.2 - - - +
98A SER* 1.3 59.7 + - - +
107A VAL* 4.4 1.0 - - - +
108A ARG* 3.6 0.7 - - - -
109A VAL* 2.7 50.7 + - + +
111A TYR* 4.7 5.1 - - + -
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Residues in contact with SER 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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39A GLU 4.3 0.4 - - - -
40A TRP* 3.1 12.8 - - - -
41A LYS* 2.9 49.8 + - - +
43A THR* 5.4 1.7 + - - -
96A LEU* 4.0 3.4 + - - -
97A LEU* 1.3 75.6 - - - +
99A CYS* 1.3 63.8 + - - +
105A GLU* 3.9 17.7 - - - -
107A VAL 3.4 11.7 - - - -
108A ARG* 4.3 14.0 + - - -
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Residues in contact with CYS 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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38A LEU* 4.0 6.7 - - - -
39A GLU 3.2 10.3 - - - -
40A TRP* 3.4 48.9 - - + -
98A SER* 1.3 78.3 - - - +
100A SER* 1.3 69.2 + - - +
105A GLU* 3.6 4.5 - - - +
106A PHE* 3.0 52.9 + - + -
107A VAL* 2.9 16.5 + - + +
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Residues in contact with SER 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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37A ASP 4.5 0.4 + - - -
38A LEU* 3.2 10.9 - - - +
39A GLU* 3.0 45.0 + - - +
41A LYS* 5.6 4.0 - - - -
99A CYS* 1.3 77.5 - - - +
101A TYR* 1.3 62.3 + - - +
102A ASP 4.2 0.2 - - - -
103A GLY* 4.0 12.0 + - - -
104A ARG 3.3 24.9 - - - -
105A GLU* 3.9 5.6 - - - -
106A PHE* 3.6 3.6 - - - -
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Residues in contact with TYR 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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34A LEU* 3.3 28.6 - - + +
35A LYS* 3.0 13.5 + - - +
36A HIS* 2.8 55.5 + - + -
37A ASP 3.5 11.2 - - - -
38A LEU* 3.9 17.3 - - + -
65A VAL* 4.9 0.2 - - + -
100A SER* 1.3 75.7 - - - +
102A ASP* 1.3 76.7 + - + +
103A GLY 3.0 0.4 - - - -
104A ARG* 2.7 43.3 + - - +
106A PHE* 3.8 4.7 - - + -
151A ILE* 4.1 4.9 - - + -
153A TRP* 3.2 54.9 + + + -
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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