Contacts of the strand formed by residues 95 - 100 (chain A) in PDB entry 1SMO
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 LEU 95 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A LYS* 3.6 49.6 - - + +
41A CYS 3.6 7.6 - - - +
42A ASP* 4.7 7.2 - - + +
43A TYR* 3.4 5.8 - - - -
88A GLU 3.7 1.0 - - - +
89A ASP* 3.7 0.3 - - - +
90A TYR* 2.9 55.1 + - + +
92A ASP* 6.2 0.2 - - - +
93A HIS* 5.0 9.4 - - + -
94A GLY* 1.3 78.8 - - - +
96A LEU* 1.3 73.8 + - - +
97A ARG* 3.7 5.2 - - + +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LYS* 3.5 0.9 - - - -
41A CYS* 2.8 46.7 + - + +
43A TYR* 3.9 10.4 - - + -
53A LYS* 3.9 26.0 - - + -
54A ALA 4.5 11.0 - - - +
70A THR* 4.2 22.7 - - + -
87A LEU* 4.5 13.7 - - + -
88A GLU 3.5 19.1 - - - +
89A ASP* 4.2 7.6 - - + +
95A LEU* 1.3 72.3 - - - +
97A ARG* 1.3 59.0 + - - +
98A VAL* 4.0 12.2 + - + +
113A CYS* 4.1 27.4 - - + -
114A VAL 5.0 0.7 - - - +
125A LEU* 4.9 3.8 - - + -
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Residues in contact with ARG 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASP* 2.9 41.4 + - - +
39A VAL 3.4 7.6 - - - +
40A LYS* 3.8 16.3 - - - +
86A ILE 3.6 1.0 - - - +
87A LEU* 3.5 5.0 - - - -
88A GLU* 2.8 66.4 + - + +
90A TYR* 3.4 22.1 + - + -
95A LEU* 3.7 14.4 - - + +
96A LEU* 1.3 73.2 - - - +
98A VAL* 1.3 67.2 + - - +
99A ARG* 3.4 34.2 - - + +
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Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A LEU* 3.7 2.2 - - + +
38A ASP* 3.5 2.3 - - - +
39A VAL* 2.9 45.0 + - + +
55A TRP* 3.6 53.8 - - + +
85A ILE* 4.4 0.9 - - + -
86A ILE 3.5 2.2 - - - -
87A LEU* 3.9 21.3 - - + -
96A LEU* 4.4 9.4 - - + +
97A ARG* 1.3 78.6 - - - +
99A ARG* 1.3 74.6 + - - +
100A MET* 4.8 0.9 - - + -
113A CYS* 4.0 17.5 - - - -
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Residues in contact with ARG 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A THR* 4.0 15.9 - - + -
37A LEU 3.0 11.4 - - - +
38A ASP* 3.7 22.0 - - + +
79A PRO* 5.8 1.8 - - - +
84A ARG 3.7 0.4 - - - +
85A ILE* 3.3 7.3 - - - +
86A ILE* 2.9 69.6 + - + +
88A GLU* 3.0 26.1 + - - -
97A ARG* 3.4 36.2 - - + +
98A VAL* 1.3 73.6 - - - +
100A MET* 1.3 65.2 + - - +
101A VAL* 4.0 4.3 - - + +
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Residues in contact with MET 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A THR* 3.4 2.3 - - - -
37A LEU* 2.9 45.5 + - + +
55A TRP* 3.5 38.4 - - + +
67A LEU* 5.5 2.0 - - + -
84A ARG* 3.4 10.1 - - + +
85A ILE* 4.3 18.4 - - + -
98A VAL* 4.8 0.9 - - + -
99A ARG* 1.3 77.7 - - - +
101A VAL* 1.3 63.7 + - - +
103A LEU* 3.7 16.2 - - + +
107A ASP* 4.1 25.6 - - + +
111A TYR* 3.7 29.4 - - + +
131A LEU* 4.4 4.3 - - - -
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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