Contacts of the helix formed by residues 84 - 101 (chain B) in PDB entry 2HOF
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 ALA 84 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B GLY 3.8 1.8 + - - -
83B LEU* 1.3 75.1 - - - +
85B VAL* 1.3 65.6 + - - +
86B LYS 4.2 4.7 - - - +
87B THR* 3.0 15.6 + - - +
88B ILE* 3.1 11.8 + - - +
129B GLU* 3.4 17.5 - - - +
13C T 2.9 45.5 + - - +
14C A 4.5 5.2 - - - +
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Residues in contact with VAL 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU 3.8 0.4 + - - -
84B ALA* 1.3 70.5 - - - +
86B LYS* 1.3 57.3 + - + +
88B ILE* 3.3 11.9 + - - +
89B GLN* 2.9 50.6 + - + +
117B MET* 4.3 4.0 - - + +
120B ILE* 4.2 2.7 - - + +
121B ARG* 3.9 36.6 - - + +
124B ASN* 3.5 24.0 - - + +
125B VAL* 5.1 4.9 - - + +
129B GLU* 2.8 31.7 + - - +
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Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B ALA* 3.1 2.2 - - - +
85B VAL* 1.3 75.7 - - + +
87B THR* 1.3 61.3 + - - +
89B GLN* 3.6 24.0 + - - +
90B GLN* 3.1 25.3 + - - +
129B GLU* 4.6 0.6 + - - -
13C T 4.1 10.1 - - + +
14C A 3.4 57.1 + - + +
15C G 2.7 47.8 + - - -
16C C 4.2 8.2 - - - +
21D G 4.5 2.2 + - - -
22D C 4.5 2.4 - - - +
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Residues in contact with THR 87 (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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83B LEU* 3.8 28.0 - - + -
84B ALA* 3.0 10.7 + - - +
86B LYS* 1.3 73.5 - - - +
88B ILE* 1.3 66.2 + - - +
90B GLN* 3.2 2.4 + - - +
91B HIS* 3.0 44.2 + - + +
12C A 3.5 14.4 - - + +
13C T 2.7 56.1 + - + +
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Residues in contact with ILE 88 (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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75B LEU* 4.0 29.9 - - + +
78B LEU* 3.9 22.9 - - + -
79B GLN* 3.7 27.6 - - + +
83B LEU* 3.6 25.4 - - + +
84B ALA 3.1 10.8 + - - +
85B VAL* 3.6 7.4 - - - +
87B THR* 1.3 75.2 - - - +
89B GLN* 1.3 61.0 + - - +
91B HIS* 3.3 3.6 + - - +
92B LEU* 3.1 21.1 + - - +
117B MET* 3.9 22.2 - - + -
120B ILE* 3.7 19.7 - - + -
124B ASN* 4.7 0.9 - - - +
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Residues in contact with GLN 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B VAL* 2.9 35.8 + - - +
86B LYS* 3.6 33.6 + - - +
88B ILE* 1.3 77.2 - - - +
90B GLN* 1.3 50.8 + - - +
92B LEU* 3.5 4.8 + - - +
93B GLY* 2.7 32.4 + - - -
117B MET* 3.8 26.2 - - + +
121B ARG* 4.7 5.1 - - - +
19D A 3.9 18.6 + - - -
20D T 4.7 19.8 - - + +
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Residues in contact with GLN 90 (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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44B MET* 4.0 16.1 - - + +
48B VAL* 4.6 2.5 - - + -
86B LYS 3.1 14.2 + - - +
87B THR 3.2 9.1 + - - +
89B GLN* 1.3 72.8 - - - +
91B HIS* 1.3 60.6 + - + +
93B GLY* 3.8 2.3 - - - +
94B GLN* 2.8 65.8 + - + +
13C T 3.3 34.2 + - + +
14C A 2.9 19.5 - - - +
22D C 4.5 8.7 - - - +
23D T 2.7 29.2 + - - +
24D A 3.8 1.6 - - - +
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Residues in contact with HIS 91 (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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44B MET* 5.7 1.6 - - - +
47B SER* 5.7 1.3 - - - -
48B VAL* 3.5 37.1 - - + +
51B SER* 3.8 17.7 - - - -
74B TYR* 2.7 32.3 + - + -
75B LEU* 4.7 0.7 - - + -
78B LEU* 3.7 25.7 - - + +
81B ARG* 6.0 0.4 - - - -
83B LEU* 4.9 0.2 - - - +
87B THR* 3.0 43.2 + - + +
88B ILE 3.3 6.9 + - - +
90B GLN* 1.3 79.7 - - + +
92B LEU* 1.3 62.7 + - - +
94B GLN 3.5 0.2 + - - -
95B LEU* 3.2 24.7 + - - +
11C T 6.2 0.6 - - - +
12C A 4.8 11.4 + - - -
13C T 4.9 5.2 - - + +
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Residues in contact with LEU 92 (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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71B VAL* 4.2 10.3 - - + -
75B LEU* 4.1 20.4 - - + +
88B ILE 3.1 12.6 + - - +
89B GLN* 3.6 8.5 - - - +
91B HIS* 1.3 76.2 - - - +
93B GLY* 1.3 56.8 + - - +
95B LEU* 3.2 7.5 + - + +
96B ASN* 2.8 43.7 + - - +
107B PRO* 4.3 2.7 - - + -
108B SER* 3.7 21.5 - - - +
113B VAL* 3.4 27.6 - - + +
114B SER* 5.9 0.4 - - - -
117B MET* 3.6 37.5 - - + -
20D T 5.1 5.4 - - - +
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Residues in contact with GLY 93 (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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89B GLN 2.7 20.6 + - - -
90B GLN* 3.8 2.9 - - - -
92B LEU* 1.3 73.4 - - - +
94B GLN* 1.3 58.4 + - - +
96B ASN* 3.4 10.5 + - - +
97B MET* 3.0 28.8 + - - +
21D G 5.7 13.1 - - - +
22D C 6.1 4.7 - - - -
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Residues in contact with GLN 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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41B THR* 4.0 7.7 + - - +
44B MET* 3.8 14.4 - - - +
45B LEU* 3.4 35.5 - - + +
48B VAL* 3.7 31.2 - - + -
90B GLN* 2.8 42.9 + - - +
91B HIS 3.9 0.2 - - - +
92B LEU 3.3 0.2 - - - -
93B GLY* 1.3 73.1 - - - +
95B LEU* 1.3 61.9 + - - +
97B MET* 3.4 20.2 + - - +
98B LEU* 3.0 29.6 + - - +
22D C 5.5 2.0 - - - -
23D T 3.8 18.8 - - - +
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Residues in contact with LEU 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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48B VAL* 4.3 11.7 - - + -
49B CYS* 5.0 6.7 - - - -
52B TRP* 3.8 40.6 - - + +
71B VAL* 4.4 16.4 - - + -
74B TYR* 4.2 26.2 - - + -
75B LEU* 5.6 0.2 - - + -
91B HIS 3.2 19.5 + - - +
92B LEU* 3.5 9.2 - - + +
94B GLN* 1.3 72.3 - - - +
96B ASN* 1.3 64.8 + - - +
98B LEU* 3.4 15.4 + - + +
99B HIS* 2.7 40.6 + - - +
107B PRO* 4.1 16.2 - - + -
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Residues in contact with ASN 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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92B LEU* 2.8 31.7 + - - +
93B GLY* 3.6 9.3 - - - +
95B LEU* 1.3 73.2 - - - +
97B MET* 1.3 51.7 + - - +
99B HIS* 3.4 1.2 + - - -
100B ARG* 2.8 37.7 + - - +
106B ARG* 3.4 23.5 - - + +
107B PRO* 3.3 16.7 - - - +
108B SER* 3.0 48.7 + - - -
20D T 5.0 4.0 + - - +
21D G 4.5 8.0 + - - +
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Residues in contact with MET 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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30B MET* 3.8 26.9 - - + +
37B PHE* 4.9 1.6 - - - -
41B THR* 4.0 15.5 - - + -
42B TRP* 6.1 0.9 - - + -
45B LEU* 3.7 22.2 - - + -
93B GLY 3.0 17.9 + - - +
94B GLN* 3.4 24.7 - - - +
95B LEU 3.3 0.2 - - - -
96B ASN* 1.3 73.4 - - - +
98B LEU* 1.3 66.9 - - - +
100B ARG* 4.5 8.3 - - - +
101B ARG* 2.9 39.2 + - + +
21D G 5.7 3.4 - - + -
22D C 3.6 46.7 - - - +
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Residues in contact with LEU 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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27B LEU* 4.4 20.2 - - + +
30B MET* 6.0 6.7 - - - +
45B LEU* 4.3 20.9 - - + -
49B CYS* 3.9 25.1 - - - -
63B TRP* 4.0 12.3 - - + -
64B PHE* 3.8 30.3 - - + -
94B GLN 3.0 17.4 + - - +
95B LEU* 3.8 9.6 - - + +
97B MET* 1.3 80.1 - - - +
99B HIS* 1.3 60.5 + - + +
101B ARG* 4.0 1.7 - - - +
102B SER* 2.8 31.5 + - - -
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Residues in contact with HIS 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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63B TRP 5.0 0.4 + - - -
64B PHE* 3.6 27.7 - + - -
65B PRO* 4.0 2.4 - - + +
66B ALA* 3.1 50.6 + - + +
95B LEU* 2.7 37.7 + - - +
96B ASN 3.9 2.5 - - - +
98B LEU* 1.3 80.2 - - + +
100B ARG* 1.4 58.9 + - - +
102B SER* 3.2 5.4 + - - -
103B GLY 3.1 4.3 + - - -
104B LEU* 2.7 45.5 + - + +
105B PRO 3.7 22.3 + - - +
106B ARG* 4.1 1.3 - - - -
107B PRO* 3.7 15.1 - - + +
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Residues in contact with ARG 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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96B ASN 2.8 21.9 + - - +
97B MET* 4.1 8.6 - - - +
99B HIS* 1.4 71.9 - - - +
101B ARG* 1.3 81.5 + - - +
103B GLY* 3.2 16.5 + - - -
104B LEU 3.8 8.9 + - - +
106B ARG* 3.9 19.9 - - + +
21D G 3.8 43.2 + - - -
22D C 2.8 29.9 + - - -
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Residues in contact with ARG 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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26B ASN* 3.4 24.8 - - - +
27B LEU* 4.9 2.8 - - - +
30B MET* 3.8 40.1 - - + +
37B PHE* 3.7 24.3 - - - -
97B MET* 2.9 23.4 + - + +
98B LEU 4.0 1.8 - - - +
100B ARG* 1.3 92.2 - - + +
102B SER* 1.4 61.2 + - - +
103B GLY* 3.3 1.3 - - - -
22D C 3.1 35.9 + - - -
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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
------------------------------------------------------------
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