Contacts of the helix formed by residues 99 - 104 (chain F) in PDB entry 1W88
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 ARG 99 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143E ILE* 6.1 3.2 - - - +
94F CYS 2.8 20.0 + - - +
95F GLY* 3.4 20.3 + - - +
96F GLN 2.7 7.0 + - - +
98F ALA* 1.3 81.0 - - - +
100F ILE* 1.3 55.5 + - - +
101F ARG 3.5 1.8 - - - -
102F TYR* 3.5 5.6 + - - +
103F ARG* 2.8 58.8 + - + +
139F GLN* 3.2 19.1 + - - +
84H GLY 5.0 4.6 + - - -
87H TYR* 2.7 38.5 + - - -
130H ASP* 3.8 29.3 + - - -
132H LEU* 5.1 1.0 - - - +
297H VAL* 3.7 37.6 - - + +
298H TYR* 6.0 0.2 - - - +
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Residues in contact with ILE 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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138E LEU* 5.7 6.3 - - + -
150E GLN* 4.8 3.6 - - - +
67F ILE* 3.7 30.5 - - + -
71F LEU* 5.1 3.1 - - + -
96F GLN* 3.2 28.5 + - + +
97F MET* 3.6 1.4 + - - -
99F ARG* 1.3 75.7 - - - +
101F ARG* 1.3 66.2 + - - +
103F ARG* 4.1 19.7 - - - +
104F THR* 2.9 35.3 + - + +
108F TYR* 4.0 23.6 - - + -
110F MET* 3.8 38.1 - - + -
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Residues in contact with ARG 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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346E ILE* 3.3 17.1 - - - +
347E MET 3.8 10.5 - - - +
348E PHE 3.6 17.9 + - - -
349E GLU* 3.5 40.6 + - - +
97F MET 4.9 1.8 + - - -
98F ALA 5.2 2.1 + - - +
99F ARG 3.5 0.6 - - - -
100F ILE* 1.3 78.7 - - - +
102F TYR* 1.3 62.7 + - - +
105F GLY 3.2 2.8 + - - -
106F GLY* 2.7 53.0 + - - -
108F TYR 3.4 13.7 - - - +
109F HIS* 3.3 32.2 + - - +
110F MET* 5.5 1.0 - - - +
164F ASN 3.5 7.3 + - - -
165F ASP* 2.8 29.4 + - - +
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Residues in contact with TYR 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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126E PHE* 4.8 0.2 - - - +
343E LEU* 3.6 39.4 - - + +
346E ILE* 3.1 36.4 + - + +
347E MET* 3.5 31.3 + - + +
98F ALA 5.5 0.8 + - - +
99F ARG* 3.5 7.2 + - - +
101F ARG* 1.3 76.9 - - - +
103F ARG* 1.3 67.4 + - + +
104F THR 3.2 1.2 + - - -
105F GLY* 3.2 9.2 + - - -
296H THR* 4.2 3.1 - - - -
297H VAL* 3.4 42.2 + - + -
298H TYR 3.0 17.9 + - - -
299H PRO* 3.2 16.5 - - - +
300H PHE* 3.3 36.6 + + - -
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Residues in contact with ARG 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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129E ASN* 3.0 38.7 + - - +
139E PRO* 3.8 8.4 - - + +
140E PRO 5.7 5.2 - - - +
141E GLN* 4.3 11.6 + - - +
142E ILE* 4.4 25.6 - - + +
143E ILE* 5.0 5.1 - - - +
95F GLY 3.1 22.6 + - - -
96F GLN* 2.5 37.9 + - - +
99F ARG* 2.8 41.7 + - - +
100F ILE* 3.9 21.2 - - - +
101F ARG 3.3 0.2 - - - -
102F TYR* 1.3 82.8 - - + +
104F THR* 1.3 62.2 + - + +
105F GLY 3.5 0.2 - - - -
297H VAL* 5.9 1.8 - - + +
300H PHE* 4.1 8.3 - - + -
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Residues in contact with THR 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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129E ASN* 3.5 22.4 - - - +
130E GLN* 3.8 3.5 - - - -
138E LEU* 4.6 3.4 - - + -
139E PRO* 3.8 24.0 - - + -
100F ILE* 2.9 25.8 + - + +
101F ARG 3.7 0.7 + - - -
102F TYR 3.2 0.2 - - - -
103F ARG* 1.3 85.0 - - + +
105F GLY* 1.3 62.5 + - - +
107F ARG* 3.0 19.3 + - - +
108F TYR* 3.0 49.2 + - + +
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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