Contacts of the helix formed by residues 82 - 98 (chain B) in PDB entry 5SV1
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 SER 82 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51B GLN* 5.9 0.4 - - - +
54B ARG* 3.8 9.4 - - - +
58B GLU* 2.6 33.1 + - - -
78B PHE* 3.5 23.0 - - - +
79B GLY 3.1 17.8 + - - -
80B SER 3.4 0.4 - - - -
81B LYS* 1.3 79.6 - - - +
83B LEU* 1.3 63.9 + - - +
84B SER 3.4 5.0 + - - -
85B LEU* 3.5 10.3 + - - +
86B HIS* 3.4 24.1 + - - -
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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
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51B GLN* 4.3 21.3 - - + +
55B LEU* 4.7 12.1 - - + -
58B GLU* 4.0 5.1 + - - +
81B LYS 4.2 9.0 - - - +
82B SER* 1.3 73.6 + - - +
84B SER* 1.3 67.0 + - - +
86B HIS* 3.0 17.4 + - + +
87B LEU* 3.0 27.9 + - + +
122B VAL* 4.6 21.5 - - + -
126B MET* 6.3 0.9 - - + -
205B PHE* 4.1 19.7 - - + -
209B LEU* 3.8 35.7 - - + -
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 4.0 2.9 - - - +
58B GLU* 3.1 31.7 + - - +
62B LEU* 3.9 17.6 - - - +
75B ALA* 5.2 0.2 - - - -
78B PHE* 4.4 4.9 - - - -
82B SER* 3.4 1.6 + - - -
83B LEU* 1.3 78.5 - - - +
85B LEU* 1.3 56.9 + - - +
87B LEU* 3.3 3.3 + - - +
88B LEU* 2.9 36.1 + - - +
212B VAL* 3.1 36.8 - - - +
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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
----------------------------------------------------------
72B ASN* 5.5 4.3 - - - +
75B ALA* 3.2 34.3 - - + +
76B ALA* 4.7 7.2 - - - +
78B PHE* 4.5 6.8 - - + +
79B GLY 4.2 13.9 - - - +
80B SER* 5.3 3.8 - - - -
82B SER* 3.5 23.8 + - - +
83B LEU 3.2 0.4 - - - -
84B SER* 1.3 78.4 - - - +
86B HIS* 1.3 67.0 + - + +
88B LEU* 4.6 4.7 - - + -
89B ASN* 3.0 69.9 + - - +
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Residues in contact with HIS 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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80B SER 3.4 23.5 + - - -
81B LYS* 4.6 7.6 - - - -
82B SER 3.4 14.5 + - - -
83B LEU* 3.0 20.9 + - + +
85B LEU* 1.3 87.1 - - + +
87B LEU* 1.3 61.5 + - + +
89B ASN* 3.4 8.4 + - + +
90B GLU* 2.9 28.1 + - - +
118B ARG* 3.6 30.2 + - - +
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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* 3.0 19.6 + - + +
84B SER* 3.3 5.4 + - - +
86B HIS* 1.3 75.2 - - + +
88B LEU* 1.3 61.7 + - - +
90B GLU* 2.8 18.2 + - - +
91B ALA* 3.0 13.2 + - - +
115B LEU* 3.7 26.0 - - + +
118B ARG* 4.0 31.2 - - + +
119B VAL* 4.7 2.5 - - + -
209B LEU* 3.8 24.2 - - + -
212B VAL* 4.2 9.0 - - + -
213B ALA* 3.6 39.0 - - + +
216B VAL* 4.3 11.4 - - + -
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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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62B LEU* 3.9 15.5 - - + -
68B LEU* 3.5 32.8 - - + +
71B ALA* 3.5 38.6 - - + +
72B ASN* 3.9 17.2 + - - +
75B ALA* 3.5 19.7 - - + -
84B SER 2.9 17.9 + - - +
85B LEU* 4.1 5.2 - - + +
87B LEU* 1.3 75.7 - - - +
89B ASN* 1.3 63.5 + - - +
91B ALA* 3.3 2.6 + - - +
92B GLN* 2.9 23.7 + - - +
216B VAL* 3.5 26.0 - - + -
219B LEU* 5.6 0.2 - - + -
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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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72B ASN* 4.1 11.1 - - - +
85B LEU* 3.0 54.6 + - - +
86B HIS* 3.7 10.4 - - + +
87B LEU 3.2 0.2 - - - -
88B LEU* 1.3 76.4 - - - +
90B GLU* 1.3 58.3 + - - +
92B GLN* 3.8 6.4 - - - +
93B ASN* 2.9 29.5 + - - +
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Residues in contact with GLU 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 HIS 2.9 8.8 + - - +
87B LEU 2.8 11.0 + - - +
89B ASN* 1.3 75.0 - - - +
91B ALA* 1.3 65.0 + - - +
93B ASN* 3.2 6.1 + - + +
94B GLU* 3.0 22.5 + - - +
111B THR* 5.6 0.2 - - - -
114B ARG* 3.2 67.5 + - + +
115B LEU* 4.0 9.2 - - + +
118B ARG* 3.1 42.9 + - - +
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Residues in contact with ALA 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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68B LEU* 5.3 7.2 - - + -
87B LEU 3.0 6.5 + - - -
88B LEU* 3.8 5.2 - - - +
90B GLU* 1.3 76.0 - - - +
92B GLN* 1.3 63.3 + - - +
94B GLU* 3.0 5.2 + - - +
95B LEU* 3.0 21.1 + - - +
111B THR* 4.1 14.1 - - + -
115B LEU* 4.6 1.9 - - + +
216B VAL* 3.7 29.2 - - + -
220B GLN* 3.3 28.8 - - + +
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Residues in contact with GLN 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B LEU* 4.6 6.7 - - - +
72B ASN* 3.7 26.1 + - - +
88B LEU 2.9 17.4 + - - +
89B ASN* 3.8 8.7 - - - +
91B ALA* 1.3 76.8 - - - +
93B ASN* 1.3 56.9 + - - +
95B LEU* 3.0 25.7 + - - +
96B GLU* 2.9 51.2 + - - +
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Residues in contact with ASN 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 ASN 2.9 20.2 + - - +
90B GLU* 3.7 6.3 - - - +
92B GLN* 1.3 76.0 - - - +
94B GLU* 1.3 58.2 + - - +
96B GLU* 3.9 13.4 + - - +
97B LEU* 2.9 48.2 + - - +
114B ARG* 3.0 27.5 + - - +
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Residues in contact with GLU 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 GLU 3.0 12.2 + - - +
91B ALA* 3.0 9.4 + - - +
93B ASN* 1.3 75.1 - - - +
95B LEU* 1.3 65.3 + - - +
97B LEU 4.5 0.4 - - - +
98B SER* 3.1 34.7 + - - -
107B ILE* 4.5 3.1 - - + +
110B ARG* 2.9 37.6 + - - +
111B THR* 3.6 33.2 - - - +
114B ARG* 3.1 26.1 + - - +
218C LEU* 5.2 0.6 - - - +
222C ARG* 2.5 36.0 + - - -
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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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68B LEU* 4.4 11.9 - - + -
91B ALA 3.0 15.8 + - - +
92B GLN* 3.0 31.1 + - - +
94B GLU* 1.3 78.4 - - - +
96B GLU* 1.3 61.2 + - + +
98B SER* 3.5 3.6 + - - -
99B GLU* 3.3 24.7 + - - +
107B ILE* 4.0 28.4 - - + +
220B GLN* 4.2 20.4 - - + +
223B ASP* 6.5 1.1 - - + -
224B LEU* 4.2 23.3 - - + -
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Residues in contact with GLU 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 GLN* 2.9 45.4 + - - +
93B ASN* 3.9 13.6 + - - +
95B LEU* 1.3 75.9 - - - +
97B LEU* 1.3 67.7 + - + +
99B GLU* 3.3 23.2 + - - +
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Residues in contact with LEU 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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93B ASN* 2.9 45.0 + - - +
94B GLU 4.5 0.9 - - - +
96B GLU* 1.3 78.1 - - + +
98B SER* 1.3 59.4 + - - +
99B GLU 3.3 2.5 + - - +
114B ARG* 4.7 1.3 - - - +
66C ARG* 5.6 14.1 - - + +
222C ARG* 3.6 47.5 - - - +
226C LEU* 4.2 16.5 - - - +
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Residues in contact with SER 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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94B GLU* 3.1 23.1 + - - -
95B LEU 3.8 3.6 - - - -
96B GLU 3.1 1.2 - - - -
97B LEU* 1.3 73.8 - - - +
99B GLU* 1.3 68.1 + - - +
100B GLY 3.1 0.2 + - - -
101B SER* 2.9 23.6 + - - -
107B ILE* 3.7 26.6 - - - +
110B ARG* 2.7 28.1 + - - -
222C ARG* 3.7 6.2 - - - +
226C LEU* 4.3 7.9 - - - -
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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
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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