Contacts of the strand formed by residues 67 - 80 (chain C) in PDB entry 4SBV
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 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60C LEU* 4.9 11.2 - - + -
61C ARG 3.8 7.4 - - - +
62C SER* 3.8 19.1 + - - -
65C ASP 3.8 1.2 + - - -
66C VAL* 1.3 75.8 - - - +
68C ILE* 1.3 77.1 + - - +
69C LEU* 4.9 3.1 - - + -
107C TRP* 3.6 38.1 + - + +
249C ARG* 3.4 1.0 - - - -
250C LEU* 2.6 48.7 + - + -
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Residues in contact with ILE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C MET 3.7 1.0 - - - +
60C LEU* 3.6 3.1 - - - -
61C ARG* 2.8 66.6 + - - +
63C SER 6.3 0.2 - - - +
66C VAL* 4.7 8.7 - - + -
67C THR* 1.3 79.0 - - - +
69C LEU* 1.3 68.1 - - - +
70C SER* 4.6 2.7 - - - +
113C VAL* 4.9 7.0 - - + -
247C THR* 3.6 26.9 - - + -
248C ILE 3.6 2.0 - - - +
249C ARG* 3.5 39.0 - - + +
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Residues in contact with LEU 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C MET 3.4 7.0 - - - +
60C LEU* 3.3 28.5 - - + -
67C THR* 4.2 1.1 - - + -
68C ILE* 1.3 78.4 - - - +
70C SER* 1.3 89.6 + - - +
71C HIS* 4.1 9.6 - - + -
99C TRP* 4.2 12.3 - - + -
100C LEU* 3.7 21.5 - - + -
103C VAL* 3.7 29.8 - - + -
246C TYR* 3.9 7.1 - - + +
247C THR* 3.2 3.5 - - - +
248C ILE* 2.9 47.4 + - + +
250C LEU* 4.7 11.2 - - + +
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Residues in contact with SER 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57C PRO 4.9 0.9 - - - +
58C PRO* 3.9 0.7 - - - +
59C MET* 2.9 49.4 + - - +
68C ILE* 5.1 2.2 - - - -
69C LEU* 1.3 71.9 - - - +
71C HIS* 1.3 63.0 + - - +
246C TYR 3.2 3.2 + - - -
247C THR* 2.4 40.0 + - - +
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Residues in contact with HIS 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 5.3 6.5 - - + -
56C ARG 3.3 26.4 + - - -
57C PRO* 4.6 0.4 + - + -
58C PRO* 3.7 34.7 - - + +
69C LEU* 4.1 7.2 - - + -
70C SER* 1.3 75.5 - - - +
72C CYS* 1.3 85.0 + - - +
73C GLU* 3.7 21.2 + - - +
99C TRP* 3.8 18.6 - + - +
245C SER* 3.4 2.9 - - - -
246C TYR* 3.1 52.2 + - + +
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Residues in contact with CYS 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 3.6 33.8 - - + +
71C HIS* 1.3 100.0 + - - +
73C GLU* 1.3 70.1 - - - +
170C PHE 5.4 0.2 - - - +
171C VAL* 3.7 31.6 - - - +
243C TYR* 4.3 7.4 - - - -
244C ALA 3.0 19.1 - - - +
245C SER* 3.9 10.5 - - - -
246C TYR* 4.2 0.9 - - - -
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Residues in contact with GLU 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 4.6 5.2 - - + -
71C HIS* 3.7 13.9 - - + +
72C CYS* 1.3 75.2 - - - +
74C LEU* 1.3 66.7 + - - +
96C VAL* 4.6 3.1 - - + +
97C GLY* 3.5 20.9 - - - -
98C THR* 2.9 10.3 + - - +
99C TRP* 2.3 44.0 + - - +
100C LEU 3.0 2.2 + - - -
243C TYR* 3.5 8.2 - - - +
244C ALA* 2.9 31.1 + - + +
246C TYR* 2.5 35.2 + - + +
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Residues in contact with LEU 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55C LEU* 5.1 2.5 - - + +
73C GLU* 1.3 83.9 - - - +
75C SER* 1.3 77.7 + - - +
76C THR 3.4 21.8 - - - +
77C GLU* 5.1 8.5 - - + +
96C VAL 5.0 1.8 - - - +
97C GLY* 5.6 1.0 - - - -
98C THR* 4.9 5.9 + - - -
241C ARG* 4.3 20.9 - - + +
242C LEU 3.4 11.9 - - - +
243C TYR* 3.5 35.1 - - + +
244C ALA* 5.8 0.2 - - - -
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Residues in contact with SER 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C GLU 3.8 1.0 + - - -
74C LEU* 1.3 77.9 - - - +
76C THR* 1.3 66.4 + - - +
89C GLU* 4.4 13.3 + - - +
95C THR 5.3 1.2 + - - -
96C VAL* 4.1 17.1 + - - -
117C TYR* 4.3 17.2 - - - -
242C LEU* 2.8 30.4 + - - +
244C ALA* 4.5 10.3 - - - -
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Residues in contact with THR 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LEU* 3.4 10.3 - - - +
75C SER* 1.3 86.2 + - - +
77C GLU* 1.3 80.6 - - - +
78C LEU* 3.4 26.5 - - + -
87C THR* 5.9 2.0 - - - +
89C GLU* 4.0 17.7 + - - +
241C ARG* 3.5 0.3 - - - +
242C LEU* 3.0 37.3 + - + +
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Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C LEU* 5.1 7.6 - - + +
76C THR* 1.3 82.0 - - - +
78C LEU* 1.3 74.9 + - - +
79C ALA 4.4 0.2 + - - -
240C GLY 4.1 6.5 - - - +
241C ARG* 4.1 18.6 - - + -
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C THR* 3.4 21.3 - - + -
77C GLU* 1.3 86.9 - - - +
79C ALA* 1.3 64.0 + - - +
87C THR* 5.2 9.6 - - + +
119C TYR* 4.8 6.5 - - + -
131C ILE* 4.2 9.0 - - + -
226C THR* 3.8 18.4 - - + -
228C MET* 3.1 40.4 - - + -
238C ASN* 3.8 3.3 - - - +
239C THR* 3.0 21.9 + - - -
240C GLY 3.2 23.2 + - - +
241C ARG* 4.3 0.6 - - - +
242C LEU* 4.5 20.9 - - + +
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Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78C LEU* 1.3 80.2 - - - +
80C VAL* 1.3 61.1 + - - +
81C THR* 5.0 2.4 - - - +
85C VAL* 5.9 2.3 - - - +
228C MET* 4.0 15.8 - - - +
236C ALA* 4.3 15.4 - - + +
237C VAL 3.0 18.4 - - - +
238C ASN* 3.4 21.3 - - - +
239C THR* 3.9 2.7 - - - +
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Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA* 1.3 71.9 - - - +
81C THR* 1.3 66.9 + - - +
128C SER 3.7 9.4 - - - +
129C GLY* 4.5 2.5 - - - -
130C ALA 4.2 4.5 - - - +
161C VAL* 4.1 22.0 - - + -
228C MET* 3.7 21.3 - - + -
229C GLU 3.5 15.7 - - - +
231C GLY* 3.4 38.3 - - - +
235C THR 4.2 0.9 - - - +
236C ALA* 3.3 4.8 - - - -
237C VAL* 2.6 47.1 + - + +
239C THR* 4.3 6.6 + - - +
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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
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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