Contacts of the helix formed by residues 79 - 96 (chain B) in PDB entry 3SRF
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 THR 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLY* 1.3 74.8 - - - -
80B HIS* 1.3 66.6 + - - +
81B GLU* 3.6 13.2 + - - +
82B TYR* 3.2 21.1 + - - +
83B HIS* 3.1 27.2 + - - -
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Residues in contact with HIS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B PHE* 4.3 10.8 - + - -
79B THR* 1.3 75.6 - - - +
81B GLU* 1.3 62.0 + - - +
83B HIS* 4.8 1.8 - - - +
84B ALA* 3.1 18.0 + - - +
223B LYS* 6.1 0.4 - - - -
226B GLN* 3.2 35.9 + - + +
227B ASP* 2.9 28.0 + - - -
230B PHE* 3.1 47.9 - + + +
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Residues in contact with GLU 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B THR* 3.2 10.6 + - - +
80B HIS* 1.3 75.7 - - - +
82B TYR* 1.3 65.4 + - - +
84B ALA* 3.2 7.5 + - - +
85B GLU* 3.2 25.0 + - + +
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Residues in contact with TYR 82 (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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50B ILE 5.6 4.3 - - - -
51B GLY* 4.2 2.8 - - - -
52B PRO* 3.8 25.8 - - - +
55B ARG* 2.8 76.2 + - - +
77B HIS 5.6 0.4 - - - -
78B GLY* 4.3 17.3 - - - -
79B THR* 3.2 20.8 + - - +
81B GLU* 1.3 79.6 - - - +
83B HIS* 1.3 75.0 + + - +
85B GLU* 3.4 2.0 + - - -
86B THR* 2.9 18.2 + - - -
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Residues in contact with HIS 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 3.6 16.7 - - + +
74B ASN 3.3 31.1 + - - -
75B PHE* 3.7 48.2 - + + -
77B HIS 2.7 23.5 + - - -
78B GLY* 3.9 3.9 + - - -
79B THR 3.1 27.4 + - - +
80B HIS* 4.1 3.8 - + - +
82B TYR* 1.3 89.3 - + - +
84B ALA* 1.3 60.7 + - - +
86B THR* 3.2 7.7 + - - -
87B ILE* 2.9 31.6 + - - +
230B PHE* 4.4 3.4 - - + -
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Residues in contact with ALA 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B HIS 3.1 19.7 + - - +
81B GLU* 3.2 6.9 + - - +
83B HIS* 1.3 76.5 - - - +
85B GLU* 1.3 57.9 + - - +
87B ILE* 3.7 8.3 + - - +
88B LYS* 3.0 26.0 + - - +
230B PHE* 3.7 17.6 - - + -
234B GLN* 3.9 14.8 - - - +
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Residues in contact with GLU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ARG* 3.3 33.1 + - - +
81B GLU* 3.2 15.5 + - + +
82B TYR* 3.6 3.0 - - - +
83B HIS 3.2 0.2 - - - -
84B ALA* 1.3 74.6 - - - +
86B THR* 1.3 59.7 + - - +
88B LYS* 3.2 10.5 + - + +
89B ASN* 2.8 51.0 + - - +
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Residues in contact with THR 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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50B ILE* 3.7 38.8 - - + +
55B ARG* 2.7 33.8 + - + +
60B LEU* 5.9 0.2 - - + -
73B LEU* 4.0 21.5 - - + -
82B TYR* 2.9 17.4 + - - -
83B HIS* 3.4 9.0 + - - -
85B GLU* 1.3 75.2 - - - +
87B ILE* 1.3 56.3 + - - +
89B ASN* 3.1 8.2 + - - +
90B VAL* 2.9 35.0 + - + +
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Residues in contact with ILE 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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73B LEU* 3.6 22.7 - - + -
75B PHE* 5.6 3.1 - - + -
83B HIS* 2.9 21.0 + - + +
84B ALA 3.7 4.3 - - - +
86B THR* 1.3 73.1 - - - +
88B LYS* 1.3 66.4 + - - +
90B VAL* 3.3 7.8 + - - +
91B ARG* 3.0 61.8 + - + +
109B VAL* 4.1 15.3 - - + -
230B PHE* 4.8 5.2 - - + -
234B GLN* 3.4 38.6 - - + +
236B VAL* 4.5 13.9 - - + -
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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
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84B ALA 3.0 16.2 + - - +
85B GLU* 3.4 15.7 - - + +
87B ILE* 1.3 77.9 - - - +
89B ASN* 1.3 59.6 + - - +
91B ARG* 3.4 5.2 + - - +
92B THR* 2.7 46.5 + - - +
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Residues in contact with ASN 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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55B ARG* 2.7 37.1 + - - +
56B SER* 3.9 2.4 - - - +
57B VAL* 3.6 29.1 - - + +
60B LEU* 3.6 7.4 - - + +
85B GLU* 2.8 33.8 + - - +
86B THR* 3.4 8.7 - - - +
88B LYS* 1.3 81.0 + - - +
90B VAL* 1.3 64.4 + - - +
92B THR* 3.2 4.1 + - - -
93B ALA* 3.0 25.3 + - - +
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Residues in contact with VAL 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ILE* 4.6 7.2 - - + -
60B LEU* 3.8 30.3 - - + -
64B ILE* 5.0 0.8 - - + +
68B MET* 5.2 1.3 - - + -
71B ALA* 4.2 28.0 - - + -
73B LEU* 5.1 3.8 - - + -
86B THR* 2.9 28.8 + - + +
87B ILE* 3.3 7.6 + - - +
89B ASN* 1.3 72.3 - - - +
91B ARG* 1.3 56.5 + - + +
93B ALA* 3.3 3.0 + - - +
94B THR* 2.7 42.7 + - - +
107B VAL* 4.5 13.5 - - + +
109B VAL* 4.5 17.5 - - + -
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Residues in contact with ARG 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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87B ILE* 3.0 46.0 + - + +
88B LYS* 3.9 4.7 - - - +
90B VAL* 1.3 73.7 - - + +
92B THR* 1.3 63.4 + - - +
94B THR* 3.9 6.1 - - - -
95B GLU* 3.1 34.9 + - + +
109B VAL* 4.4 25.7 - - + +
234B GLN* 2.7 33.6 + - - +
235B ASP* 3.0 24.3 + - - +
236B VAL* 4.6 1.4 - - - +
237B ASP* 5.4 1.0 + - - -
460B ARG* 5.9 7.1 - - - +
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Residues in contact with THR 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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57B VAL* 3.9 21.8 - - + +
61B LYS* 5.9 0.4 - - - -
88B LYS* 2.7 40.4 + - - +
89B ASN* 3.2 7.9 + - - -
91B ARG* 1.3 74.5 - - - +
93B ALA* 1.3 64.7 + - - +
95B GLU* 3.5 4.5 + - - +
96B SER* 3.3 21.2 + - - -
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Residues in contact with ALA 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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57B VAL* 3.8 8.9 - - + +
60B LEU* 3.6 28.5 - - + -
61B LYS* 3.7 24.5 - - + +
64B ILE* 3.9 5.4 - - + -
89B ASN 3.0 15.8 + - - +
90B VAL 3.7 3.6 - - - +
92B THR* 1.3 77.0 - - - +
94B THR* 1.3 58.0 + - - +
96B SER* 2.6 22.6 + - - -
97B PHE* 3.2 13.3 - - - -
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Residues in contact with THR 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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64B ILE* 3.8 15.3 - - + +
90B VAL* 2.7 25.8 + - - +
91B ARG* 4.0 7.6 - - - -
93B ALA* 1.3 74.0 - - - +
95B GLU* 1.3 66.0 + - - +
96B SER 3.1 5.6 + - - -
97B PHE* 3.2 15.5 + - - +
104B TYR* 3.6 33.5 - - - +
105B ARG 3.7 18.1 - - - +
107B VAL* 3.8 27.1 + - + +
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Residues in contact with GLU 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 ARG* 3.1 22.3 + - + +
92B THR* 3.5 4.0 + - - +
94B THR* 1.3 78.5 - - - +
96B SER* 1.3 55.8 + - - +
97B PHE 3.1 6.1 - - - -
98B ALA* 3.1 38.3 + - + +
99B SER 4.5 1.0 + - - -
104B TYR* 3.5 22.7 + - - -
474B LYS* 5.8 1.2 + - - -
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Residues in contact with SER 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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61B LYS* 3.6 30.8 - - - +
92B THR 3.3 11.6 + - - -
93B ALA 2.6 21.9 + - - -
94B THR 3.1 0.2 - - - -
95B GLU* 1.3 77.0 - - - +
97B PHE* 1.3 70.7 + - - +
98B ALA 3.4 1.1 - - - -
99B SER* 4.7 7.7 + - - -
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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