Contacts of the helix formed by residues 80 - 96 (chain B) in PDB entry 3DC1
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 80 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B ARG* 3.8 9.2 - - - +
75B SER* 3.9 26.5 - - - -
76B PRO* 4.5 2.0 - - + -
79B GLY* 1.3 75.2 - - - -
81B PRO* 1.4 62.3 - - + +
82B GLU* 3.8 20.0 - - + +
83B LEU* 3.1 18.4 + - + +
84B LEU* 2.7 32.4 + - - +
297B THR* 4.1 12.3 - - + -
300B GLN* 2.8 28.8 + - + +
301B LEU* 3.5 35.2 - - + -
304B SER* 4.1 10.5 - - - -
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Residues in contact with PRO 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B ARG* 4.0 7.4 - - - +
76B PRO* 4.5 14.1 - - + -
79B GLY 3.6 4.2 - - - +
80B ILE* 1.4 86.7 - - + +
82B GLU* 1.3 66.2 + - - +
84B LEU* 3.7 11.3 - - + +
85B SER* 2.7 36.7 + - - -
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Residues in contact with GLU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B MET* 6.0 0.3 - - - +
70B ARG* 2.9 44.9 + - - -
80B ILE* 3.8 9.7 - - + +
81B PRO* 1.3 89.2 - - - +
83B LEU* 1.3 61.9 + - - +
85B SER* 3.4 6.0 + - - -
86B TRP* 3.2 14.2 + - - +
301B LEU* 4.5 3.9 - - + +
304B SER* 3.2 23.8 - - - +
308B HIS* 3.0 29.7 + - + +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B ILE* 3.1 19.9 + - + +
82B GLU* 1.3 77.8 - - - +
84B LEU* 1.3 60.7 + - - +
86B TRP* 3.9 3.1 - - + -
87B LEU* 2.9 52.6 + - + +
113B VAL* 3.8 28.0 - - + -
261B PHE* 5.7 0.7 - - + -
271B ILE* 4.3 11.4 - - + -
300B GLN* 4.0 24.9 - - + +
303B ILE* 3.9 6.5 - - + -
304B SER* 3.5 25.6 + - - +
307B LEU* 3.7 30.1 - - + -
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Residues in contact with LEU 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B PRO* 6.2 0.2 - - + -
78B ALA* 3.8 30.3 - - + +
79B GLY* 3.6 20.2 - - - +
80B ILE 2.7 19.5 + - - +
81B PRO* 3.7 10.5 - - + +
83B LEU* 1.3 73.8 - - - +
85B SER* 1.3 63.1 + - - +
87B LEU* 4.0 1.0 - - - +
88B LYS* 3.0 43.2 + - - +
111B LEU* 3.3 45.1 - - + +
113B VAL* 4.4 3.5 - - + +
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Residues in contact with SER 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81B PRO 2.7 23.5 + - - -
82B GLU* 3.4 9.9 + - - -
84B LEU* 1.3 72.6 - - - +
86B TRP* 1.3 60.1 + - - +
88B LYS* 3.6 7.7 - - - +
89B GLN* 2.9 39.0 + - - +
308B HIS* 4.8 4.7 - - - -
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Residues in contact with TRP 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B GLU 3.2 17.7 + - - +
83B LEU* 4.0 6.1 - - + +
85B SER* 1.3 81.6 + - - +
87B LEU* 1.3 64.8 + - + +
89B GLN* 3.5 7.0 + - - +
90B LEU* 2.8 48.4 + - + -
261B PHE* 5.4 0.7 - + - -
307B LEU* 3.3 58.2 + - + -
308B HIS* 3.4 37.0 - + + +
311B GLY* 3.7 22.0 - - - -
312B GLU* 3.9 21.3 + - + +
315B PHE* 4.0 28.7 - + + -
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Residues in contact with LEU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B LEU* 2.9 40.5 + - + +
86B TRP* 1.3 82.6 - - + +
88B LYS* 1.3 53.3 + - - +
90B LEU* 3.1 9.0 + - + +
91B GLN* 2.7 38.6 + - - +
111B LEU* 3.8 20.6 - - + -
113B VAL* 3.7 27.1 - - + -
261B PHE* 3.6 34.8 - - + -
271B ILE* 6.2 0.4 - - + -
273B PHE* 3.6 33.7 - - + -
307B LEU* 4.6 0.2 - - + -
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Residues in contact with LYS 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84B LEU* 3.0 34.1 + - - +
85B SER* 3.6 6.7 - - - +
87B LEU* 1.3 74.0 - - - +
89B GLN* 1.3 53.7 + - - +
91B GLN* 2.9 7.1 + - - +
92B ILE* 2.7 40.7 + - + +
109B MET* 4.4 21.6 + - + +
110B ASP* 3.3 28.8 + - - +
111B LEU* 3.9 31.6 - - + +
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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
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85B SER* 2.9 24.0 + - - +
86B TRP* 3.7 7.4 - - - +
88B LYS* 1.3 73.2 - - - +
90B LEU* 1.3 59.4 + - - +
92B ILE* 3.6 21.0 + - - +
93B LYS* 2.9 35.9 + - + +
312B GLU* 4.1 12.1 - - - +
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Residues in contact with LEU 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B TRP* 2.8 39.3 + - + +
87B LEU* 3.3 12.8 - - + +
89B GLN* 1.3 71.4 - - - +
91B GLN* 1.3 62.3 + - - +
93B LYS* 3.1 4.0 + - - +
94B LEU* 3.0 66.9 + - + +
235B PHE* 4.2 13.2 - - + -
261B PHE* 5.1 1.3 - - + -
273B PHE* 4.4 22.4 - - + -
312B GLU* 4.0 16.2 + - + +
315B PHE* 3.9 27.4 - - + -
316B MET* 5.1 2.2 - - + -
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B LEU 2.7 20.6 + - - +
88B LYS* 2.9 7.1 + - - +
90B LEU* 1.3 76.0 - - - +
92B ILE* 1.3 63.1 + - - +
94B LEU* 4.3 8.8 - - - +
95B HIS* 3.1 43.8 + - - +
96B ASN 3.4 4.2 + - - -
97B PRO* 3.6 3.5 - - - +
109B MET* 4.2 15.9 - - - -
111B LEU* 3.6 17.5 - - + -
235B PHE* 5.8 0.7 - - - -
247B LEU* 3.8 6.2 - - + +
257B ARG* 3.3 13.9 - - - +
259B ASP* 3.0 25.9 + - - +
273B PHE* 3.9 9.9 - - + -
275B THR* 2.9 23.9 + - - +
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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
----------------------------------------------------------
88B LYS* 2.7 22.9 + - + +
89B GLN* 4.0 22.4 - - - +
91B GLN* 1.3 73.0 - - - +
93B LYS* 1.3 62.7 + - + +
96B ASN* 3.1 31.2 + - - +
97B PRO* 4.2 1.6 - - + -
100B ILE* 3.6 51.6 - - + -
101B HIS* 5.8 0.2 - - - +
109B MET* 4.5 7.2 - - + -
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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 GLN* 2.9 25.7 + - + +
90B LEU* 3.1 4.2 + - - +
92B ILE* 1.3 79.0 - - + +
94B LEU* 1.3 68.1 + - + +
96B ASN* 4.7 0.7 - - - -
312B GLU* 3.4 28.2 + - - +
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Residues in contact with LEU 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 LEU* 3.0 49.5 + - + +
91B GLN* 4.3 3.1 - - - +
93B LYS* 1.3 86.6 - - + +
95B HIS* 1.3 89.4 + - + +
234B TYR* 4.0 15.5 + - + +
235B PHE* 3.9 23.3 - - + -
242B ARG* 4.6 15.1 + - - +
248B SER* 5.5 0.2 - - - -
316B MET* 4.7 11.9 - - + -
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Residues in contact with HIS 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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91B GLN* 3.1 32.9 + - - +
93B LYS 3.5 0.2 - - - -
94B LEU* 1.3 97.8 + - + +
96B ASN* 1.3 73.3 + - - +
97B PRO* 3.2 11.3 - - + -
234B TYR* 3.0 29.5 - + - -
244B PRO* 6.1 0.2 - - - +
245B THR* 3.0 38.0 + - + +
247B LEU* 4.0 15.3 - - + -
248B SER* 3.1 35.2 - - - +
257B ARG* 3.8 16.5 + - - -
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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 ILE* 3.1 23.8 + - - +
93B LYS 5.8 0.2 - - - -
95B HIS* 1.3 78.1 - - - +
97B PRO* 1.3 74.6 - - - +
98B PRO* 3.4 6.5 - - - +
100B ILE* 4.4 16.8 - - - +
248B SER 4.6 1.6 - - - +
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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
------------------------------------------------------------
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