Contacts of the strand formed by residues 98 - 104 (chain F) in PDB entry 6S1M
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 98 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91F ARG 4.8 0.2 - - - +
92F ALA* 4.4 12.3 - - - +
93F GLU 4.5 0.2 + - - -
96F ALA* 3.1 30.6 + - + +
97F ASP* 1.3 81.4 - - - +
99F LEU* 1.3 67.6 + - - +
100F ALA* 4.3 0.3 + - - +
115F GLU* 4.0 20.0 + - - +
116F MET 3.3 14.8 + - - -
117F LYS* 4.6 4.7 - - - -
118F LEU* 3.5 8.1 - - - +
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Residues in contact with LEU 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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2F PHE* 4.7 3.8 - - + -
28F TRP* 6.5 1.6 - - + -
68F MET* 4.1 17.3 - - + -
70F VAL* 5.1 4.9 - - + -
75F MET* 5.0 8.1 - - + -
90F LEU* 4.5 20.4 - - + -
91F ARG 3.3 29.6 - - - +
92F ALA* 3.8 11.0 - - + -
98F THR* 1.3 75.7 + - - +
100F ALA* 1.3 68.4 + - - +
101F LEU* 4.3 10.3 - - + -
114F TYR 3.8 0.2 - - - +
115F GLU* 3.5 2.6 - - - -
116F MET* 2.7 62.4 + - + +
118F LEU* 3.7 17.6 - - + +
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Residues in contact with ALA 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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89F THR 3.1 6.3 - - - +
90F LEU* 3.5 3.1 - - - -
91F ARG* 2.9 57.2 + - + +
98F THR 4.3 0.2 + - - -
99F LEU* 1.3 76.7 - - - +
101F LEU* 1.3 62.6 + - - +
102F VAL* 5.2 0.9 - - + -
113F ASP* 4.6 3.8 - - - +
114F TYR 3.3 3.6 - - - -
115F GLU* 3.6 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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75F MET* 4.6 9.4 - - + -
78F ILE* 4.0 12.6 - - + -
79F LEU* 3.7 35.7 - - + -
88F ILE* 5.0 0.4 - - + -
89F THR 3.7 3.4 - - - -
90F LEU* 4.2 19.3 - - + -
99F LEU* 4.3 14.4 - - + +
100F ALA* 1.3 77.2 - - - +
102F VAL* 1.3 60.9 + - - +
103F PHE* 3.8 18.8 - - + -
112F SER 3.8 0.5 - - - +
113F ASP* 3.5 1.2 - - - -
114F TYR* 2.6 52.9 + - + +
116F MET* 4.2 30.5 - - + -
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Residues in contact with VAL 102 (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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87F ILE 3.4 3.3 - - - +
88F ILE* 3.4 1.6 - - - -
89F THR* 2.8 45.6 + - - +
91F ARG* 3.7 26.7 - - + +
100F ALA 5.2 2.2 - - - -
101F LEU* 1.3 72.4 - - - +
103F PHE* 1.3 66.4 + - - +
104F GLU* 4.4 14.1 - - + +
111F VAL* 3.7 21.8 - - + -
112F SER 3.2 9.9 - - - +
113F ASP* 3.2 26.5 - - + +
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Residues in contact with PHE 103 (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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78F ILE* 3.9 14.1 - - + -
79F LEU* 4.0 9.2 - - + -
81F CYS 3.6 18.4 - - - -
82F ALA* 3.7 17.5 - - + -
86F ASP* 4.0 19.1 - - + +
87F ILE 3.3 2.9 - - - -
88F ILE* 3.5 35.9 - - + -
101F LEU* 3.8 35.2 - - + -
102F VAL* 1.3 79.0 - - - +
104F GLU* 1.3 62.3 + - - +
105F ALA 4.0 0.9 + - - -
110F LYS 4.2 0.2 - - - +
111F VAL* 3.4 5.7 - - - +
112F SER* 2.8 40.4 + - - +
114F TYR* 3.6 31.4 - + - -
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Residues in contact with GLU 104 (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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5F ARG* 3.3 38.2 + - - -
86F ASP* 3.2 3.6 - - - -
87F ILE* 2.7 51.9 + - + +
89F THR* 4.1 7.6 + - - -
102F VAL* 4.4 9.7 - - + +
103F PHE* 1.3 76.9 - - - +
105F ALA* 1.3 68.2 + - - +
106F PRO 3.6 0.5 - - - -
110F LYS 4.1 3.8 - - - +
111F VAL* 4.3 20.6 - - + -
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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