Contacts of the strand formed by residues 102 - 108 (chain C) in PDB entry 1H9D
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 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100C GLY 3.3 5.2 + - - +
101C THR* 1.3 78.5 - - - +
103C VAL* 1.3 68.2 + - - +
104C THR* 4.2 7.9 - - + -
121C THR* 4.1 21.8 - - + +
122C ALA 3.4 19.1 - - - +
123C ALA* 4.6 2.2 - - + +
153C PHE* 2.9 56.5 + - + +
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Residues in contact with VAL 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C VAL* 4.2 10.5 - - + -
101C THR 3.9 8.7 - - - +
102C LEU* 1.3 79.2 - - - +
104C THR* 1.3 69.4 + - - +
121C THR* 3.6 0.5 - - - -
122C ALA 2.7 34.6 + - - +
124C MET* 4.0 12.3 - - + -
129C ALA* 3.6 24.5 - - + -
131C PHE* 3.7 16.4 - - + -
150C ILE* 3.9 22.4 - - + -
151C THR 3.2 11.7 - - - +
152C VAL* 4.0 19.1 - - + -
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Residues in contact with THR 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C LEU* 4.2 11.4 - - + -
103C VAL* 1.3 81.2 - - - +
105C VAL* 1.3 69.9 + - - +
106C MET* 4.7 5.7 - - - +
120C ALA* 3.1 9.4 - - - -
121C THR* 3.9 15.0 - - - +
131C PHE* 4.3 0.7 - - - -
149C THR 3.6 0.7 + - - +
150C ILE* 3.4 7.1 - - - +
151C THR* 3.0 34.2 + - - -
153C PHE* 3.6 29.0 - - + -
65D SER* 4.3 7.1 + - - +
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Residues in contact with VAL 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C PHE* 3.8 23.8 - - + -
104C THR* 1.3 80.5 - - - +
106C MET* 1.3 77.8 + - - +
117C LEU* 3.1 24.5 - - + +
120C ALA* 3.1 21.3 + - + +
131C PHE* 3.7 21.3 - - + -
134C LEU* 4.6 14.1 - - + -
136C PHE* 5.1 1.8 - - + -
148C LEU* 4.3 23.8 - - + -
149C THR 3.4 4.9 - - - +
150C ILE* 4.4 9.9 - - + -
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Residues in contact with MET 106 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C THR* 4.7 7.0 - - - +
105C VAL* 1.3 79.8 - - - +
107C ALA* 1.3 62.8 + - - +
117C LEU* 3.7 6.5 - - - -
148C LEU* 3.3 5.2 - - - +
149C THR* 2.7 37.9 + - + +
151C THR* 4.1 12.8 - - - +
30D THR* 5.2 1.8 - - - -
54D GLU* 4.9 15.9 - - - +
55D ILE 6.4 0.2 - - - -
63D ASN* 3.5 32.5 - - + +
64D LEU* 3.0 16.2 - - - +
65D SER* 2.9 50.7 - - - +
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Residues in contact with ALA 107 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C MET* 1.3 77.7 - - - +
108C GLY* 1.3 59.3 + - - +
114C SER* 3.6 0.7 - - - -
115C ALA* 3.0 32.3 + - + +
117C LEU* 4.2 8.7 - - + +
136C PHE* 4.3 10.1 - - + -
146C PHE* 4.0 17.7 - - + -
147C THR 3.4 5.8 - - - -
148C LEU* 3.7 20.9 - - + -
63D ASN* 3.1 17.0 + - - +
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Residues in contact with GLY 108 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ALA* 1.3 78.1 - - - +
109C ASN* 1.3 61.6 + - - +
112C ASN 3.4 13.9 - - - -
113C TYR 3.8 3.8 - - - -
115C ALA 4.3 0.4 - - - -
146C PHE* 3.5 9.9 - - - -
147C THR* 2.8 32.5 + - - +
61D GLY 3.1 18.7 + - - -
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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