Contacts of the strand formed by residues 112 - 119 (chain B) in PDB entry 1H8F
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 112 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45B GLY* 3.4 19.8 - - - -
46B GLN* 3.6 19.9 + - - +
98B LEU* 3.7 28.0 - - + -
101B MET* 3.9 26.9 + - + +
102B ARG* 4.2 13.2 - - + +
110B VAL 4.0 1.0 + - - -
111B ARG* 1.3 73.4 + - - +
113B ARG* 1.3 62.3 + - - +
114B TYR 3.2 24.7 - - - +
115B PHE* 4.2 8.3 - - + -
130B LEU* 3.7 31.6 - - + -
131B VAL 3.9 3.8 - - - +
132B LEU* 3.9 15.9 - - + +
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B PRO* 3.6 1.6 - - - +
45B GLY 2.9 18.9 + - - -
75B LEU* 3.7 22.3 - - - +
80B GLU* 2.7 45.2 + - - +
82B VAL* 3.6 23.9 - - - +
111B ARG* 3.4 18.3 + - + +
112B LEU* 1.3 73.1 - - - +
114B TYR* 1.3 93.1 + - + +
131B VAL* 2.8 15.9 + - + +
133B ASP* 2.6 38.0 + - - +
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Residues in contact with TYR 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 3.5 22.0 - - + -
43B THR 3.3 9.0 - - - +
44B PRO* 4.0 17.3 - - + -
45B GLY 4.2 0.9 - - - +
52B GLN* 3.6 25.5 + - - -
54B VAL* 4.0 36.1 - - + +
75B LEU* 4.7 9.6 - - + +
77B ASP* 5.4 2.8 + - - -
112B LEU* 3.2 9.4 - - - +
113B ARG* 1.3 112.3 + - + +
115B PHE* 1.3 68.6 + - - +
131B VAL* 3.0 41.6 + - + -
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Residues in contact with PHE 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B ALA* 4.2 0.4 - - - -
43B THR* 3.1 67.0 + - + -
44B PRO 3.7 7.4 - - - -
49B ASP* 5.0 0.9 - - - -
98B LEU* 3.7 32.1 - - + -
102B ARG* 3.6 43.7 - - - -
112B LEU* 4.2 7.6 - - + -
114B TYR* 1.3 82.1 - - - +
116B PHE* 1.3 65.5 + - - +
117B TYR* 4.4 15.5 - + - -
128B LEU* 4.2 7.9 - - + -
129B ASN 3.1 15.0 - - - +
130B LEU* 4.0 15.0 - - + -
131B VAL 4.5 0.2 - - - +
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Residues in contact with PHE 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 4.0 34.1 - - + -
41B VAL 3.7 21.8 - - - +
42B ALA* 4.0 13.5 - - + -
56B TYR* 4.1 23.6 - + - -
84B ILE* 4.7 4.0 - - + -
115B PHE* 1.3 78.6 - - - +
117B TYR* 1.3 83.7 + - - +
118B SER* 4.5 6.7 - - - -
128B LEU* 3.7 3.3 - - - +
129B ASN* 2.8 68.3 + - + +
131B VAL* 3.7 23.1 - - + -
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Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B GLN* 4.3 10.1 - - + +
91B LYS* 3.5 31.7 + - - -
94B LYS* 5.7 2.4 + - - -
95B ASN* 5.8 1.2 - - - +
98B LEU* 4.0 13.5 - - - +
115B PHE* 4.4 15.7 - + - -
116B PHE* 1.3 87.5 - - - +
118B SER* 1.3 65.8 + - - +
126B VAL* 3.9 16.8 - - + -
127B TYR 3.2 14.6 - - - +
128B LEU* 3.7 33.4 - - + +
129B ASN* 3.9 0.9 - - - -
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B VAL* 6.4 0.2 - - - -
86B LYS* 4.0 11.6 + - - -
116B PHE* 4.5 8.1 - - - -
117B TYR* 1.3 77.8 - - - +
119B SER* 1.3 69.2 + - - +
126B VAL* 4.9 0.9 - - - -
127B TYR* 3.0 31.8 + - - +
129B ASN* 3.2 22.8 + - - -
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Residues in contact with SER 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LYS* 5.4 1.6 + - - -
118B SER* 1.3 76.8 + - - +
120B GLY* 1.3 64.5 + - - +
124B ASP* 5.3 9.0 - - - -
125B GLU 3.1 12.8 - - - -
126B VAL* 4.4 5.5 - - - +
127B TYR* 4.8 0.5 - - - -
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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