Contacts of the helix formed by residues 93 - 105 (chain B) in PDB entry 2HHL
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 LEU 93 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B SER* 1.3 76.2 - - - +
94B ALA* 1.4 55.5 + - - +
95B LYS* 3.2 35.4 - - + +
96B TYR* 3.1 10.5 + - + +
97B ALA* 2.9 29.1 + - - +
115B PHE* 4.3 2.7 - - + -
116B ARG* 3.8 52.7 - - + +
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Residues in contact with ALA 94 (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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93B LEU* 1.4 71.5 - - - +
95B LYS* 1.3 62.6 + - - +
98B ASP* 2.8 49.9 + - - +
99B PRO* 3.4 0.7 - - - +
115B PHE* 3.5 38.8 - - + +
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Residues in contact with LYS 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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54B VAL* 4.8 0.2 - - - +
55B PRO 5.1 1.6 - - - +
56B VAL* 4.0 26.1 - - + +
57B GLU* 3.0 32.3 + - + +
58B ILE* 4.4 12.2 - - - +
59B ASP* 5.1 3.8 + - - +
93B LEU* 4.1 29.8 - - + +
94B ALA* 1.3 78.2 - - - +
96B TYR* 1.3 59.7 + - + +
99B PRO* 3.4 18.0 - - - +
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Residues in contact with TYR 96 (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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35B LEU* 4.0 12.2 - - + +
36B ASP* 2.6 40.9 + - - -
40B VAL* 4.1 7.6 - - - +
42B SER* 2.6 30.5 + - - -
54B VAL* 4.5 2.4 - - + +
56B VAL* 4.1 24.0 - - + -
65B VAL* 3.9 22.2 - - + -
92B SER* 3.6 20.6 - - - -
93B LEU* 3.1 9.4 + - + +
95B LYS* 1.3 82.4 - - + +
97B ALA* 1.3 73.0 + - - +
98B ASP 3.4 0.4 - - - -
99B PRO* 3.1 12.1 - - - +
100B VAL* 3.4 29.3 + - + +
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Residues in contact with ALA 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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35B LEU* 3.7 17.2 - - + +
88B LEU* 5.3 1.8 - - + -
90B THR* 3.6 30.7 - - + -
92B SER* 4.3 0.2 - - - -
93B LEU 2.9 19.3 + - - +
96B TYR* 1.3 83.3 - - + +
98B ASP* 1.3 56.0 + - - +
100B VAL* 3.5 1.8 + - - +
101B ALA* 2.8 31.8 + - - +
115B PHE* 3.8 12.1 - - + -
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Residues in contact with ASP 98 (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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94B ALA* 2.8 30.2 + - - +
97B ALA* 1.3 70.5 - - - +
99B PRO* 1.4 63.4 - - + +
101B ALA* 3.2 1.2 + - - -
102B ASP* 2.9 31.4 + - - +
113B ARG* 2.8 41.6 + - - +
115B PHE* 3.3 20.6 - - - -
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Residues in contact with PRO 99 (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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54B VAL* 3.5 26.0 - - + -
55B PRO 5.9 0.2 - - - +
94B ALA 3.4 7.9 - - - +
95B LYS* 3.4 17.3 - - - +
96B TYR 3.1 11.7 - - - +
98B ASP* 1.4 94.3 - - + +
100B VAL* 1.4 61.0 + - - +
102B ASP* 3.2 12.4 + - + +
103B LEU* 3.2 30.7 + - + +
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Residues in contact with VAL 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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35B LEU* 4.1 26.7 - - + -
40B VAL* 4.2 11.2 - - + -
52B PHE* 4.4 4.9 - - + -
54B VAL* 4.1 11.6 - - + +
67B VAL* 4.1 35.0 - - + -
96B TYR* 3.4 39.9 + - + +
97B ALA 3.9 6.1 - - - +
99B PRO* 1.4 75.3 - - - +
101B ALA* 1.3 58.3 + - - +
103B LEU* 3.2 5.6 + - - +
104B LEU* 2.8 30.3 + - + +
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Residues in contact with ALA 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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35B LEU* 5.3 2.4 - - + +
88B LEU* 3.7 22.9 - - + -
97B ALA 2.8 21.7 + - - +
98B ASP 3.2 0.2 + - - -
100B VAL* 1.3 76.4 - - - +
102B ASP* 1.3 54.5 + - - +
104B LEU* 4.5 7.2 - - - +
105B ASP* 2.8 36.7 + - - +
110B PHE* 5.3 5.4 - - + -
113B ARG* 3.4 31.8 + - - +
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Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASP* 2.9 18.0 + - - +
99B PRO* 3.2 15.0 + - + +
101B ALA* 1.3 77.0 - - - +
103B LEU* 1.3 67.4 + - + +
105B ASP 3.6 13.9 - - - +
106B ARG* 4.4 5.5 + - - +
113B ARG* 2.9 29.1 + - - +
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Residues in contact with LEU 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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52B PHE* 3.8 51.5 - - + -
53B ILE 4.6 5.6 - - - +
54B VAL* 4.0 16.6 - - + -
99B PRO* 3.2 19.3 + - + +
100B VAL* 3.7 3.4 - - - +
102B ASP* 1.3 81.4 - - + +
104B LEU* 1.3 61.0 + - - +
106B ARG* 3.6 21.0 + - - +
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Residues in contact with LEU 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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35B LEU* 4.2 10.8 - - + -
39B LEU* 3.8 30.3 - - + -
40B VAL* 4.0 29.2 - - + -
52B PHE* 3.8 8.9 - - + -
69B LYS* 4.3 14.8 - - + +
73B VAL* 3.9 30.7 - - + -
74B ASP* 4.5 3.4 - - - +
77B LEU* 4.0 12.6 - - + +
100B VAL* 2.8 21.7 + - + +
101B ALA* 4.2 4.3 - - - +
103B LEU* 1.3 74.2 - - - +
105B ASP* 1.3 59.8 + - - +
106B ARG* 3.4 2.8 + - - +
107B TRP* 3.4 23.4 - - - -
110B PHE* 5.0 6.3 - - + -
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Residues in contact with ASP 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B LEU* 5.3 2.2 - - + -
101B ALA 2.8 20.6 + - - +
102B ASP* 3.6 11.7 - - - +
104B LEU* 1.3 71.3 - - + +
106B ARG* 1.3 59.8 + - - +
107B TRP* 3.4 7.0 + - - -
108B GLY* 3.2 11.9 + - - -
109B VAL* 2.9 34.8 + - - +
110B PHE* 2.9 54.2 + - + +
113B ARG* 4.9 9.6 + - - +
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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