Contacts of the strand formed by residues 111 - 116 (chain B) in PDB entry 4DBW
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 111 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B ARG* 4.2 1.6 - - - +
81B TYR* 3.7 31.2 - - + +
83B SER* 4.3 11.2 - - - -
99B LEU* 4.0 12.3 - - + -
102B SER* 5.7 2.5 - - - -
103B LEU* 3.6 19.5 - - + +
110B TYR* 1.3 78.9 - - - +
112B ASP* 1.3 59.9 + - - +
113B LEU 3.6 22.7 - - - +
114B TYR* 3.9 8.1 - - + -
159B LEU 3.0 9.9 + - - +
160B ALA* 3.2 23.1 - - + -
161B LYS 2.9 23.9 + - - -
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Residues in contact with ASP 112 (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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14B HIS* 5.9 0.2 - - - +
76B ARG* 3.0 25.6 + - - -
77B GLU* 5.8 0.5 - - - +
79B ILE 3.0 11.0 - - - +
80B PHE* 3.7 28.0 - - + -
81B TYR 2.8 36.4 + - - +
110B TYR* 3.5 17.8 + - - -
111B VAL* 1.3 72.8 - - - +
113B LEU* 1.3 59.1 + - - +
161B LYS* 3.5 14.7 - - + +
162B SER* 2.9 29.1 + - - -
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Residues in contact with LEU 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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16B MET* 3.7 25.8 - - + -
48B HIS* 5.4 1.3 - - - +
80B PHE* 3.6 9.4 - - + -
81B TYR 3.2 3.0 + - - -
82B THR* 3.3 30.4 - - + +
83B SER 3.1 25.3 + - - +
111B VAL* 3.2 8.0 - - - +
112B ASP* 1.3 81.6 - - - +
114B TYR* 1.3 63.4 + - - +
115B LEU* 3.6 34.8 - - + -
162B SER* 3.3 16.6 - - - +
164B GLY 4.0 2.7 - - - +
187B VAL* 3.6 25.8 - - + -
188B CYS* 3.9 5.2 - - - -
190B GLN* 5.7 1.3 - - - +
214B VAL* 6.0 0.7 - - + -
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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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53B HIS* 6.0 0.7 - - - +
83B SER* 3.5 22.7 - - - -
84B LYS 3.7 10.3 + - - -
85B LEU* 3.5 44.5 - - + +
95B VAL* 4.6 4.5 - - + -
98B ALA* 3.7 4.5 + - - +
99B LEU* 3.4 62.3 + - + -
102B SER* 4.6 3.7 + - - -
111B VAL* 3.9 11.2 - - + -
113B LEU* 1.3 74.2 - - - +
115B LEU* 1.3 62.4 + - - +
151B MET* 3.2 40.9 - - + +
154B CYS* 5.2 3.1 - - + -
160B ALA* 3.9 11.7 - - + -
162B SER 3.0 8.6 + - - +
163B ILE* 3.4 4.1 - - + -
164B GLY 3.0 21.0 + - - -
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Residues in contact with LEU 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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82B THR* 3.9 16.6 - - + -
83B SER 3.1 6.3 + - - -
84B LYS* 3.2 20.1 - - + -
85B LEU* 2.7 33.4 + - - +
113B LEU* 3.6 22.7 - - + -
114B TYR* 1.3 75.2 - - - +
116B ILE* 1.3 66.3 + - - +
151B MET* 3.9 4.7 - - - +
164B GLY* 3.2 26.9 - - - +
165B VAL 3.8 4.0 - - - +
166B SER* 4.4 1.3 - - - -
188B CYS* 3.5 22.9 - - - -
190B GLN* 3.5 39.0 - - + +
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Residues in contact with ILE 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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85B LEU* 4.2 7.2 - - + -
90B HIS* 3.6 19.5 - - + +
115B LEU* 1.3 69.4 - - - +
117B HIS* 1.3 60.2 + - - +
118B SER 3.3 25.4 + - - +
144B LEU* 4.7 10.8 - - + +
147B THR* 3.7 29.2 - - + -
148B TRP* 4.1 20.0 - - + -
151B MET* 4.0 17.3 - - + -
164B GLY 3.1 9.7 + - - +
165B VAL* 4.3 9.6 - - + -
166B SER* 2.9 29.1 + - - +
168B PHE* 4.1 20.4 - - + -
176B ILE* 6.0 1.1 - - + -
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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