Contacts of the helix formed by residues 80 - 94 (chain B) in PDB entry 3HB8
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 PHE 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ARG 4.3 0.4 + - - -
79B VAL* 1.3 72.2 - - - +
81B TRP* 1.3 57.5 + - - +
82B LYS* 3.3 21.5 - - + -
83B GLY* 2.8 41.0 + - - -
84B VAL* 3.0 16.7 + - - +
105B GLY 3.7 21.1 - - - -
106B VAL* 3.8 19.5 - - + -
108B ILE* 4.4 14.1 - - + -
225B PHE* 3.8 18.4 - + + -
314B EDO 5.5 0.9 - - - -
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Residues in contact with TRP 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B PHE* 3.7 25.4 - + - -
73B LEU* 4.2 24.9 - - + -
79B VAL* 2.6 16.4 + - - +
80B PHE* 1.3 70.3 - - - +
82B LYS* 1.3 71.0 + - + +
84B VAL* 2.9 29.3 + - + +
85B LEU* 2.9 47.8 + - + +
228B ALA* 5.0 0.7 - - + -
232B LEU* 3.7 35.7 - - + -
279B LEU* 3.8 10.8 - - + -
296B PHE* 4.5 6.3 - - + +
297B GLN* 5.9 0.6 - - - +
298B ILE* 3.5 40.6 - - + +
301B TYR* 5.3 4.0 - - + -
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 3.3 19.9 - - + -
81B TRP* 1.3 84.7 - - + +
83B GLY* 1.3 60.1 + - - +
85B LEU* 4.2 5.0 - - + +
86B GLU* 2.9 55.0 + - + +
104B LYS 4.1 17.1 + - - +
105B GLY* 5.3 4.4 + - - -
106B VAL* 4.5 3.3 - - + +
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Residues in contact with GLY 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B PHE* 2.8 38.8 + - - -
82B LYS* 1.3 79.0 - - - +
84B VAL* 1.3 53.4 + - - -
86B GLU* 4.0 0.3 - - - +
87B GLU* 2.8 38.6 + - - +
106B VAL* 3.8 12.6 - - - +
225B PHE* 3.9 7.0 - - - -
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Residues in contact with VAL 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B VAL* 4.3 3.6 - - + -
80B PHE 3.0 16.4 + - - +
81B TRP* 2.9 23.5 + - + +
83B GLY* 1.3 76.8 - - - +
85B LEU* 1.3 57.5 + - - +
87B GLU* 3.6 3.2 - - - +
88B LEU* 2.9 30.9 + - - +
225B PHE* 3.6 35.6 - - + +
228B ALA* 3.7 15.7 - - + +
229B SER* 3.2 39.7 - - - +
232B LEU* 4.5 4.5 - - + -
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B TRP* 2.9 45.4 + - + +
82B LYS* 4.2 5.6 - - + +
84B VAL* 1.3 80.3 - - - +
86B GLU* 1.3 63.5 + - + +
88B LEU* 3.8 1.7 - - - +
89B LEU* 3.1 46.2 + - + +
232B LEU* 3.8 19.3 - - + -
236B MET* 5.7 0.2 - - - -
293B ALA* 3.8 34.1 - - + +
296B PHE* 3.7 30.5 - - + -
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Residues in contact with GLU 86 (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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82B LYS* 2.9 45.1 + - + +
83B GLY 4.0 0.2 - - - +
85B LEU* 1.3 74.3 - - + +
87B GLU* 1.3 66.2 + - - +
89B LEU* 3.4 12.3 + - - +
90B TRP* 3.0 22.2 + - - +
101B LEU* 3.9 18.9 - - + +
104B LYS* 3.6 39.8 - - + +
106B VAL* 3.9 11.9 - - + -
293B ALA* 3.9 23.8 - - - +
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Residues in contact with GLU 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 GLY 2.8 20.1 + - - +
84B VAL 3.6 2.4 - - - +
86B GLU* 1.3 76.2 - - - +
88B LEU* 1.3 56.3 + - - +
90B TRP* 3.0 9.5 - - - +
91B PHE* 2.9 58.9 + - + -
101B LEU* 3.7 26.4 - - + +
108B ILE* 4.1 8.7 - - + +
109B TRP* 3.1 22.8 + - - +
135B TYR* 5.8 0.2 - - - -
225B PHE* 3.2 28.4 - - - -
229B SER* 4.1 6.8 + - - -
314B EDO 5.5 2.1 - - - -
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Residues in contact with LEU 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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84B VAL* 2.9 16.8 + - + +
85B LEU 3.8 4.5 - - - +
86B GLU 3.2 0.2 - - - -
87B GLU* 1.3 74.4 + - - +
89B LEU* 1.3 59.4 + - + +
91B PHE* 2.8 28.2 + - + +
92B ILE* 2.9 30.9 + - + +
139B TRP* 4.0 22.4 - - + -
229B SER* 3.6 22.0 - - - +
232B LEU* 3.5 33.7 - - + -
233B LEU* 3.7 18.2 - - + +
236B MET* 3.7 13.9 - - + -
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Residues in contact with LEU 89 (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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85B LEU* 3.1 40.1 + - + +
86B GLU* 3.7 13.7 - - - +
88B LEU* 1.3 75.3 - - + +
90B TRP* 1.3 57.8 + - - +
92B ILE* 3.4 15.2 + - + +
93B LYS* 3.0 42.1 + - + +
236B MET* 4.9 7.9 - - - -
291B PHE* 3.9 37.2 - - + +
292B LYS* 4.3 2.0 - - - +
293B ALA* 3.8 24.9 - - + +
296B PHE* 4.9 1.1 - - + -
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Residues in contact with TRP 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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86B GLU 3.0 14.1 + - - +
87B GLU* 3.0 15.0 - - - +
89B LEU* 1.3 76.7 - - - +
91B PHE* 1.3 95.5 + + - -
93B LYS* 3.6 14.0 + - - +
94B GLY 3.6 2.4 + - - -
95B SER* 3.0 60.4 + - - +
96B THR* 4.6 0.2 - - - -
97B ASN 3.0 33.2 + - - -
98B ALA* 4.2 2.2 - - - -
100B GLU* 3.1 25.8 - - + +
101B LEU* 3.7 28.9 - - + +
109B TRP* 4.3 18.6 - + - -
131B LEU* 3.3 26.0 - - + -
134B VAL* 4.6 10.1 - - + -
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Residues in contact with PHE 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLU* 2.9 53.9 + - + -
88B LEU* 2.8 16.6 + - + +
90B TRP* 1.3 105.7 - + - +
92B ILE* 1.3 66.2 + - - +
94B GLY* 2.9 11.4 + - - -
109B TRP* 4.6 2.5 - + - -
134B VAL* 5.8 0.2 - - + -
135B TYR* 3.6 46.7 - + + -
136B GLY* 3.2 23.5 - - - +
139B TRP* 3.8 38.0 - + + -
140B ARG* 4.6 1.4 - - - +
196B HIS* 6.0 4.9 - + - -
229B SER* 5.9 4.0 - - - -
230B TYR* 6.1 2.2 - + - -
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Residues in contact with ILE 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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88B LEU* 2.9 25.7 + - + +
89B LEU* 3.6 18.8 - - + +
91B PHE* 1.3 78.1 - - - +
93B LYS* 1.3 63.4 + - + +
94B GLY 3.1 0.9 + - - -
139B TRP* 4.5 4.9 - - + -
140B ARG* 2.8 41.7 + - - +
161B LEU* 4.0 12.3 - - + -
233B LEU* 4.9 1.1 - - + -
236B MET* 3.1 37.9 - - + -
288B ILE* 3.7 39.5 - - + +
289B ASP* 4.4 8.8 - - - +
291B PHE* 5.3 0.2 - - + -
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Residues in contact with LYS 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 LEU* 3.0 25.3 + - + +
90B TRP* 3.7 33.4 - - - +
92B ILE* 1.3 77.0 - - + +
94B GLY* 1.3 60.0 + - - +
95B SER* 4.2 7.0 - - - +
100B GLU* 3.5 27.9 + - - +
104B LYS* 4.2 18.8 - - - +
140B ARG* 5.1 1.1 - - - +
141B HIS* 5.8 1.0 + - - -
289B ASP* 5.9 2.2 - - - +
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Residues in contact with GLY 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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90B TRP 3.6 0.2 + - - -
91B PHE 2.9 16.3 + - - -
92B ILE 3.0 2.4 - - - -
93B LYS* 1.3 79.5 - - - +
95B SER* 1.3 64.1 + - - +
96B THR* 3.7 11.6 + - - +
136B GLY* 3.6 20.7 - - - +
137B PHE* 4.0 3.3 + - - -
140B ARG* 4.3 7.2 - - - -
141B HIS* 5.2 9.1 + - - -
153B TYR* 5.9 2.4 - - - -
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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