Contacts of the strand formed by residues 96 - 101 (chain F) in PDB entry 1SMK
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 VAL 96 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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203E GLU* 6.0 2.0 - - - +
71F SER 2.8 15.8 + - - +
72F VAL* 3.4 11.9 - - + +
73F LEU 2.7 29.0 + - - +
74F HIS* 5.5 0.7 - - - -
94F GLY 4.1 6.3 - - - +
95F ALA* 1.3 75.7 - - - +
97F VAL* 1.3 63.1 + - - +
98F ARG* 5.5 5.8 - - + +
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Residues in contact with VAL 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F LYS* 4.2 13.8 - - + +
73F LEU* 3.2 17.5 - - + +
75F LEU* 3.9 31.2 - - + -
85F THR* 3.7 11.4 - - + +
88F ILE* 4.0 10.5 - - + -
89F SER* 3.2 45.2 - - - +
95F ALA 3.8 1.8 + - - -
96F VAL* 1.3 80.2 - - - +
98F ARG* 1.3 69.5 + - - +
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Residues in contact with ARG 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F LEU 2.8 7.7 + - - -
74F HIS* 3.2 35.0 + - + -
75F LEU 2.7 31.5 + - - -
85F THR* 3.5 5.8 - - - -
96F VAL* 5.5 6.8 - - + +
97F VAL* 1.3 79.7 - - - +
99F GLY* 1.3 55.5 + - - +
100F PHE* 3.2 23.7 - - + -
108F ALA 5.4 1.0 + - - -
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Residues in contact with GLY 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F LEU 3.2 5.4 - - - -
81F ALA* 4.6 5.2 - - - -
82F PRO* 5.3 5.7 - - - +
85F THR* 2.9 33.1 - - - +
98F ARG* 1.3 71.5 - - - +
100F PHE* 1.3 70.8 + - - -
105F GLN* 4.5 2.8 - - - +
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Residues in contact with PHE 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F HIS* 3.2 50.5 - + + -
75F LEU 2.7 13.9 + - - +
76F TYR* 3.2 7.6 - - + -
77F ASP 3.1 24.8 + - - +
81F ALA* 3.4 6.4 - - - +
98F ARG* 3.2 38.8 - - + -
99F GLY* 1.3 76.6 - - - -
101F LEU* 1.3 60.4 + - - +
105F GLN* 3.6 27.8 - - + +
108F ALA* 3.5 26.5 - - + -
109F ALA* 3.3 26.9 - - + -
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Residues in contact with LEU 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77F ASP 3.3 3.1 - - - +
78F VAL 3.2 37.0 - - - +
79F VAL* 3.4 17.3 - - - +
80F ASN 4.1 2.0 - - - +
81F ALA 4.3 3.1 - - - +
82F PRO* 3.8 30.5 - - + -
100F PHE* 1.3 75.2 - - - +
102F GLY* 1.3 69.1 + - - +
104F GLN* 4.8 2.8 - - - +
105F GLN* 3.0 33.0 + - - +
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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