Contacts of the strand formed by residues 67 - 78 (chain B) in PDB entry 1SMV
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 67 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B GLY 3.6 9.6 - - - +
66B ALA* 1.3 76.0 - - - +
68B THR* 1.3 70.4 - - - +
69B VAL* 4.1 5.1 + - + -
107B TRP* 3.4 46.7 - - + +
248B ILE 3.8 0.3 - - - +
249B GLN* 3.6 1.3 - - - -
250B MET* 2.8 52.1 + - + +
253B PRO* 5.9 1.1 - - + -
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Residues in contact with THR 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ALA* 4.9 4.0 - - - +
67B ILE* 1.3 81.9 + - - +
69B VAL* 1.3 67.0 + - - +
70B LEU* 4.9 4.9 - - + -
113B LEU* 5.0 4.0 - - + +
247B THR* 3.9 23.1 - - + -
248B ILE 3.2 14.6 - - - +
249B GLN* 4.4 15.7 + - + +
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Residues in contact with VAL 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ILE* 4.1 5.5 + - + -
68B THR* 1.3 77.6 - - - +
70B LEU* 1.3 69.2 + - - +
99B TRP* 4.3 26.2 - - + -
100B LEU* 4.7 4.0 - - + -
103B VAL* 5.0 4.0 - - + -
246B TYR* 3.9 18.3 - - + +
247B THR* 3.3 3.5 - - - +
248B ILE* 2.8 51.0 + - + +
250B MET* 3.9 18.8 - - + -
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Residues in contact with LEU 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B THR* 4.5 5.8 + - + -
69B VAL* 1.3 72.7 - - - +
71B HIS* 1.3 68.4 + - - +
99B TRP* 6.0 0.2 - - - -
245B THR* 5.7 5.2 - - + -
246B TYR 3.3 11.7 - - - +
247B THR* 3.0 41.5 - - + +
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Residues in contact with HIS 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B VAL* 4.3 1.1 - - + -
70B LEU* 1.3 80.2 + - - +
72B CYS* 1.3 79.0 + - - +
73B GLU* 4.0 12.6 - - + +
99B TRP* 3.3 52.5 - + + -
245B THR* 3.4 4.0 - - - +
246B TYR* 2.8 63.0 + - + +
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Residues in contact with CYS 72 (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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71B HIS* 1.3 88.4 + - - +
73B GLU* 1.3 62.1 + - - +
171B ILE* 3.6 35.4 - - + +
243B TYR* 5.6 2.7 - - + -
244B ASP 3.1 6.5 - - - +
245B THR* 3.6 25.6 - - + +
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Residues in contact with GLU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B HIS* 4.0 9.9 - - + +
72B CYS* 1.3 75.7 - - - +
74B LEU* 1.3 70.3 + - - +
75B THR 3.3 0.2 + - - -
96B VAL* 5.0 2.5 - - + +
97B GLY* 3.7 13.3 - - - -
98B THR* 3.3 9.0 + - - -
99B TRP* 2.8 34.1 + - + +
100B LEU* 2.9 19.8 + - - +
243B TYR* 3.3 9.1 - - - +
244B ASP* 2.9 31.5 + - + +
246B TYR* 2.8 31.4 + - + +
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Residues in contact with LEU 74 (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 GLU* 1.3 87.1 + - - +
75B THR* 1.3 68.2 + - - +
76B ALA 3.5 20.6 - - - +
77B GLU* 3.7 26.7 - - + +
97B GLY* 4.2 5.2 - - - -
98B THR 4.9 1.0 + - - -
241B ARG* 3.8 25.8 - - + +
242B ILE 3.5 10.8 - - - +
243B TYR* 3.5 20.5 - - + -
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Residues in contact with THR 75 (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 GLU 3.3 1.0 + - - -
74B LEU* 1.3 77.0 - - - +
76B ALA* 1.3 60.1 + - + +
89B GLU* 2.8 28.9 + - - +
95B THR 4.3 2.4 + - - +
96B VAL 2.6 27.2 + - - +
97B GLY* 4.8 2.1 - - - -
117B TYR* 4.1 5.8 - - + -
242B ILE* 2.8 54.9 + - + +
243B TYR 3.8 7.9 - - - -
244B ASP* 3.9 13.7 - - + +
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Residues in contact with ALA 76 (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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74B LEU* 3.5 4.5 - - - +
75B THR* 1.3 83.1 - - + +
77B GLU* 1.3 67.5 + - - +
78B ILE* 4.3 8.5 - - + +
89B GLU* 4.7 6.5 - - - +
226B ILE* 5.3 7.0 - - + -
241B ARG* 3.3 3.3 - - - -
242B ILE* 2.7 47.8 + - + +
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Residues in contact with GLU 77 (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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74B LEU* 3.7 21.9 - - + +
76B ALA* 1.3 77.9 - - - +
78B ILE* 1.3 68.2 + - - +
79B GLY 4.2 0.7 + - - -
240B GLY 3.9 3.4 - - - +
241B ARG* 3.0 37.9 + - + -
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Residues in contact with ILE 78 (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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76B ALA* 4.3 7.9 - - + +
77B GLU* 1.3 81.7 - - - +
79B GLY* 1.3 61.4 + - - +
119B TYR* 4.1 18.2 - - + -
131B ILE* 4.7 0.4 - - + -
226B ILE* 4.8 6.7 - - + -
228B LEU* 3.3 46.7 - - + -
238B ALA* 3.8 4.0 - - - +
239B ALA* 2.9 25.0 + - + -
240B GLY 2.7 26.6 + - - +
242B ILE* 3.7 38.6 - - + -
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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