Contacts of the helix formed by residues 82 - 98 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C ARG* 3.9 13.9 - - - +
58C GLU* 2.7 40.5 + - - -
78C PHE* 4.0 5.3 - - - +
79C GLY* 3.4 28.1 + - - -
80C SER 3.5 0.6 - - - +
81C LYS* 1.3 80.4 - - - +
83C LEU* 1.3 61.3 + - - +
84C SER 3.3 4.9 + - - -
85C LEU* 3.6 10.0 + - - +
86C HIS* 3.5 24.1 + - - -
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Residues in contact with LEU 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51C GLN* 5.1 14.4 - - - +
54C ARG* 4.9 3.2 - - - +
55C LEU* 4.7 16.6 - - + -
58C GLU* 4.4 1.4 + - - -
81C LYS 4.5 6.7 - - - +
82C SER* 1.3 74.2 + - - +
84C SER* 1.3 66.7 + - - +
85C LEU 3.3 0.2 - - - -
86C HIS* 3.0 15.7 + - + +
87C LEU* 3.0 26.6 + - + +
122C VAL* 4.6 20.6 - - + -
125C GLN* 6.1 2.9 - - - +
205C PHE* 3.9 23.3 - - + -
209C LEU* 3.8 32.1 - - + -
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Residues in contact with SER 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 3.9 15.4 - - - +
58C GLU* 3.1 26.8 + - - +
62C LEU* 4.3 20.9 - - - +
78C PHE* 4.4 7.4 - - - -
82C SER* 3.3 1.8 + - - -
83C LEU* 1.3 77.2 - - - +
85C LEU* 1.3 57.5 + - - +
87C LEU* 3.1 9.0 + - - +
88C LEU* 2.9 34.9 + - - +
212C VAL* 3.9 18.2 - - - +
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Residues in contact with LEU 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ASN* 5.4 5.2 - - - +
75C ALA* 3.2 35.7 - - + +
76C ALA* 4.7 9.6 - - - +
78C PHE* 4.7 4.3 - - + -
79C GLY 3.7 19.7 - - - +
80C SER* 5.3 5.4 - - - +
82C SER* 3.6 20.2 + - - +
83C LEU 3.3 0.6 - - - -
84C SER* 1.3 78.5 - - - +
86C HIS* 1.3 60.5 + - + +
88C LEU* 4.6 5.4 - - + +
89C ASN* 2.8 59.0 + - - +
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Residues in contact with HIS 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C SER 4.0 17.1 + - - -
81C LYS* 4.4 11.1 + - - -
82C SER 3.5 16.8 + - - -
83C LEU* 3.0 19.3 + - + +
85C LEU* 1.3 82.0 - - + +
87C LEU* 1.3 63.4 + - + +
89C ASN* 3.6 11.9 + - + +
90C GLU* 2.9 31.9 + - - +
118C ARG* 3.7 27.3 + - - +
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Residues in contact with LEU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C LEU* 3.0 18.1 + - + +
84C SER* 3.1 6.7 + - - +
86C HIS* 1.3 77.3 - - + +
88C LEU* 1.3 65.7 + - - +
90C GLU* 2.9 13.6 + - + +
91C ALA* 2.9 12.8 + - - +
115C LEU* 3.7 28.6 - - + +
118C ARG* 4.4 23.8 - - + +
119C VAL* 5.2 1.3 - - + -
209C LEU* 3.6 31.6 - - + -
212C VAL* 3.9 12.6 - - + -
213C ALA* 3.8 30.5 - - + +
216C VAL* 4.5 10.3 - - + -
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Residues in contact with LEU 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C LEU* 3.9 20.6 - - + -
68C LEU* 4.0 27.7 - - + +
71C ALA* 3.9 24.2 - - + +
72C ASN* 3.8 17.5 + - - +
75C ALA* 3.7 29.4 - - + -
84C SER 2.9 15.2 + - - +
85C LEU* 4.2 5.2 - - + +
87C LEU* 1.3 76.2 - - - +
89C ASN* 1.3 58.6 + - - +
91C ALA* 3.3 5.5 + - - +
92C GLN* 2.9 28.1 + - - +
216C VAL* 3.6 28.0 - - + -
219C LEU* 5.8 0.4 - - + -
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Residues in contact with ASN 89 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ASN* 4.5 7.8 + - - -
85C LEU* 2.8 55.3 + - - +
86C HIS* 3.8 14.4 - - + +
88C LEU* 1.3 77.7 - - - +
90C GLU* 1.3 57.4 + - - +
92C GLN* 3.5 8.2 + - - +
93C ASN* 2.9 28.2 + - - +
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Residues in contact with GLU 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86C HIS 2.9 11.1 + - - +
87C LEU* 2.9 9.2 + - - +
89C ASN* 1.3 75.0 - - - +
91C ALA* 1.3 64.8 + - - +
93C ASN* 4.4 2.5 - - + -
94C GLU* 3.0 6.4 + - - +
111C THR* 5.5 0.2 - - - +
114C ARG* 2.7 66.9 + - + +
115C LEU* 4.1 13.5 - - + -
118C ARG* 3.2 46.3 + - - +
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Residues in contact with ALA 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 4.9 13.9 - - + -
87C LEU 2.9 6.6 + - - +
88C LEU* 3.6 7.2 - - - +
90C GLU* 1.3 73.6 - - - +
92C GLN* 1.3 65.7 + - - +
94C GLU* 3.1 2.9 + - - +
95C LEU* 2.9 28.5 + - - +
111C THR* 4.4 15.5 - - + -
115C LEU* 4.7 2.3 - - + +
216C VAL* 3.7 29.6 - - + -
220C GLN* 4.3 13.0 - - - +
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Residues in contact with GLN 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 4.8 6.2 - - - +
72C ASN* 3.8 22.9 - - - +
88C LEU 2.9 16.9 + - - +
89C ASN* 3.6 10.8 - - - +
91C ALA* 1.3 74.7 - - - +
93C ASN* 1.3 58.1 + - - +
95C LEU* 3.2 16.3 + - - +
96C GLU* 2.9 63.0 + - - +
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Residues in contact with ASN 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ASN 2.9 17.6 + - - +
90C GLU* 3.7 1.8 - - - +
91C ALA 3.2 0.2 - - - -
92C GLN* 1.3 78.1 - - - +
94C GLU* 1.3 56.8 + - - +
96C GLU* 3.8 12.7 + - - +
97C LEU* 3.0 54.5 + - - +
114C ARG* 3.0 33.4 + - - +
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Residues in contact with GLU 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLU 3.0 9.2 + - - +
91C ALA 3.1 6.9 + - - +
93C ASN* 1.3 74.6 - - - +
95C LEU* 1.3 65.1 + - - +
97C LEU* 4.5 0.7 - - - +
98C SER* 3.1 43.1 + - - +
107C ILE* 4.4 4.8 - - + +
110C ARG* 3.1 25.7 + - + +
111C THR* 3.4 35.7 - - - +
114C ARG* 3.1 30.8 + - - +
218D LEU* 4.7 0.5 - - - +
222D ARG* 2.9 30.7 + - - -
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Residues in contact with LEU 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68C LEU* 4.5 14.8 - - + -
91C ALA 2.9 16.9 + - - +
92C GLN* 3.6 21.1 - - - +
94C GLU* 1.3 77.6 - - - +
96C GLU* 1.3 63.0 + - + +
98C SER* 3.4 3.7 + - - -
99C GLU* 3.2 27.6 + - - +
107C ILE* 4.0 27.8 - - + +
220C GLN* 4.1 20.9 - - + +
224C LEU* 4.2 22.7 - - + -
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Residues in contact with GLU 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92C GLN* 2.9 51.4 + - - +
93C ASN* 3.8 12.0 + - - +
95C LEU* 1.3 75.4 - - + +
97C LEU* 1.3 68.3 + - + +
98C SER 3.3 0.7 + - - -
99C GLU* 3.3 24.4 + - - +
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Residues in contact with LEU 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93C ASN* 3.0 44.3 + - - +
94C GLU* 3.8 2.4 + - - +
96C GLU* 1.3 78.4 - - + +
98C SER* 1.3 58.4 + - - +
99C GLU 3.3 1.1 + - - +
114C ARG* 4.4 5.8 - - - +
66D ARG* 6.6 0.2 - - + -
222D ARG* 3.3 55.8 - - - +
226D LEU* 4.2 10.4 - - - +
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Residues in contact with SER 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94C GLU* 3.1 34.4 + - - -
95C LEU 3.7 2.2 - - - -
96C GLU 3.1 0.8 - - - -
97C LEU* 1.3 76.1 - - - +
99C GLU* 1.3 65.5 + - - +
100C GLY 3.3 0.2 + - - -
101C SER* 3.0 23.0 + - - -
107C ILE* 3.6 29.7 - - - +
110C ARG* 3.3 19.5 + - - -
222D ARG* 3.7 7.8 - - - +
226D LEU* 4.0 5.7 - - - +
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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