Contacts of the helix formed by residues 102 - 113 (chain B) in PDB entry 2HQR
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 102 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B GLU* 4.1 31.2 - - + +
16B ILE* 4.1 27.1 - - + -
19B GLY* 4.4 20.2 - - - -
99B TYR* 4.0 24.1 - - + +
101B SER* 1.3 73.1 - - - +
103B LYS* 1.3 69.0 + - + +
104B ALA 2.9 3.3 - - - +
105B LEU* 2.6 32.5 + - - +
106B VAL* 2.9 14.8 + - + +
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Residues in contact with LYS 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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84A VAL* 4.9 7.4 - - + -
19B GLY* 6.0 5.4 - - - -
22B VAL* 6.4 2.7 - - - -
23B LYS* 6.5 0.9 - - - -
101B SER* 2.2 27.6 + - - +
102B ILE* 1.3 81.0 - - + +
104B ALA* 1.3 52.6 + - - +
106B VAL* 4.5 7.4 - - - +
107B ALA* 2.7 37.4 + - - +
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Residues in contact with ALA 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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80A SER* 4.3 11.9 - - - -
83A GLU* 3.2 39.1 - - + +
84A VAL* 4.5 6.0 - - + +
95B ILE* 6.1 0.4 - - - -
100B ARG* 3.8 9.6 - - + +
101B SER* 3.3 24.5 + - - +
102B ILE 2.9 0.6 - - - -
103B LYS* 1.3 79.8 - - - +
105B LEU* 1.3 62.2 + - - +
107B ALA* 3.7 6.3 - - - +
108B ARG* 3.2 17.0 + - - +
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Residues in contact with LEU 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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16B ILE* 3.7 31.4 - - + -
49B MET* 3.6 30.5 - - + -
72B LEU* 3.8 17.7 - - + -
95B ILE* 3.7 40.8 - - + -
99B TYR* 3.8 18.4 - - + -
100B ARG 5.7 0.4 - - - +
101B SER 5.2 0.2 - - - +
102B ILE* 2.6 19.8 + - - +
104B ALA* 1.3 71.7 - - - +
106B VAL* 1.3 67.5 + - + +
108B ARG* 3.1 14.2 + - - +
109B ILE* 3.2 21.3 + - + +
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 5.4 6.1 - - + -
19B GLY* 4.0 8.5 - - - +
20B LEU* 3.9 32.1 - - + +
23B LYS* 3.4 44.4 - - + +
102B ILE* 2.9 21.7 + - + +
103B LYS* 4.2 5.4 - - - +
105B LEU* 1.3 80.9 - - + +
107B ALA* 1.3 52.8 + - - +
109B ILE* 2.7 16.6 + - + -
110B GLU* 2.7 33.5 + - - +
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Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 6.2 0.9 - - + -
84A VAL* 4.0 25.4 - - + -
87A PHE* 5.5 6.7 - - + +
23B LYS* 4.5 2.0 - - - +
103B LYS* 2.7 28.0 + - + +
104B ALA* 3.7 4.9 - - - +
106B VAL* 1.3 73.0 - - - +
108B ARG* 1.3 62.6 + - - +
110B GLU* 3.1 15.6 + - - +
111B ALA* 3.1 23.7 + - - +
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Residues in contact with ARG 108 (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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83A GLU* 4.7 7.0 - - - +
87A PHE* 3.1 51.0 - - + -
92A ASP 4.1 12.3 + - - -
93A ASP* 4.7 10.5 + - - -
108A ARG* 6.1 0.2 - - - +
112A ARG* 5.1 8.7 - - - +
72B LEU* 5.6 0.2 - - + -
92B ASP* 5.4 2.0 + - - -
93B ASP* 4.2 31.6 - - - +
95B ILE* 4.6 16.8 - - + +
104B ALA 3.2 10.1 + - - +
105B LEU* 3.1 11.5 + - - +
106B VAL 3.1 0.2 - - - -
107B ALA* 1.3 79.6 - - - +
109B ILE* 1.3 63.2 + - + +
111B ALA* 4.1 4.0 - - - +
112B ARG* 3.2 55.6 + - - +
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Residues in contact with ILE 109 (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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3B VAL* 5.2 14.4 - - + -
5B LEU* 6.3 0.2 - - + -
16B ILE* 6.4 2.0 - - + -
20B LEU* 6.0 3.8 - - + -
25B PHE* 5.2 12.8 - - + -
47B LEU* 4.1 33.4 - - + -
49B MET* 4.9 7.2 - - - -
72B LEU* 3.7 28.7 - - + -
93B ASP* 5.9 0.7 - - - -
105B LEU* 3.4 23.1 - - + +
106B VAL* 2.7 25.8 + - + +
108B ARG* 1.3 72.0 - - - +
110B GLU* 1.3 68.2 + - - +
112B ARG* 3.3 6.5 - - - +
113B LEU* 3.3 22.9 + - + +
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Residues in contact with GLU 110 (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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23B LYS* 2.5 45.1 + - + +
25B PHE* 6.1 2.5 - - - -
106B VAL* 2.7 9.9 + - - +
107B ALA* 3.1 13.2 + - - +
109B ILE* 1.3 69.9 - - - +
111B ALA* 1.3 68.3 + - - +
113B LEU 2.9 25.7 + - - -
114B ARG* 3.3 36.7 + - + +
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Residues in contact with ALA 111 (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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87A PHE* 4.3 34.1 - - + +
107B ALA 3.1 11.3 + - - +
108B ARG* 4.3 4.9 - - - +
110B GLU* 1.3 81.0 - - - +
112B ARG* 1.3 68.6 + - - +
113B LEU* 3.3 0.9 + - - -
114B ARG* 4.8 13.4 + - - +
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Residues in contact with ARG 112 (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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92A ASP 5.9 1.0 + - - -
112A ARG* 6.1 2.4 - - - +
47B LEU* 5.2 1.3 - - + -
70B VAL* 4.2 15.5 - - + +
92B ASP* 3.3 31.5 + - - -
93B ASP* 4.8 9.0 - - - -
108B ARG* 3.2 40.8 + - - +
109B ILE* 3.3 15.3 - - - +
110B GLU 3.0 0.6 + - - -
111B ALA* 1.3 84.2 + - - +
113B LEU* 1.3 77.7 + - + +
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Residues in contact with LEU 113 (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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1B MET* 4.6 0.7 - - - -
25B PHE* 3.9 34.1 - - + -
46B ASP* 3.3 27.4 - - + +
47B LEU* 4.4 14.4 - - + -
70B VAL* 4.2 18.6 - - + -
109B ILE* 3.3 11.3 + - + +
110B GLU* 2.9 8.5 + - - +
112B ARG* 1.3 103.8 - - + +
114B ARG* 1.3 64.4 + - - +
116B TRP* 4.0 26.1 - - + +
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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