Contacts of the strand formed by residues 181 - 187 (chain B) in PDB entry 4QKH
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 LYS 181 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ARG* 6.1 0.9 - - - +
90B SER* 3.3 26.0 + - - +
91B ASP* 3.7 16.3 - - - +
92B ASP 3.5 15.3 - - - +
93B THR* 3.7 12.0 - - + +
129B SER* 3.2 33.0 + - - -
130B ASP 3.4 12.2 + - - +
131B HIS* 3.2 20.9 - - + +
132B TRP* 2.7 29.0 + - - -
180B ARG* 1.3 80.4 - - - +
182B TRP* 1.3 55.8 + - - +
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Residues in contact with TRP 182 (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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88B TYR* 3.7 6.5 - + - +
90B SER* 2.9 58.1 + - - -
92B ASP* 3.4 33.4 - - + -
94B LYS* 3.5 37.5 - - + -
99B SER* 3.6 32.1 + - - +
102B PHE* 3.4 53.2 - + + -
103B CYS* 3.7 22.2 - - - -
110B LEU* 3.8 9.4 - - + -
131B HIS* 3.7 4.9 - - - -
132B TRP* 3.8 8.7 - - + +
180B ARG 4.1 1.6 - - - -
181B LYS* 1.3 79.3 - - - +
183B ILE* 1.3 66.5 - - - +
184B CYS* 3.6 7.6 - - - -
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Residues in contact with ILE 183 (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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87B PHE* 4.2 13.0 - - + -
88B TYR 3.1 10.8 - - - +
89B PHE* 3.6 29.2 - - + -
110B LEU* 3.5 9.5 - - - +
111B ALA* 2.8 38.5 + - + +
122B LEU* 4.2 12.1 - - + -
126B LYS* 4.9 2.7 - - + -
131B HIS* 3.7 28.0 - - + -
132B TRP 3.1 9.1 + - - +
133B ILE* 4.6 5.2 - - + -
166B LEU* 4.2 22.4 - - + -
182B TRP* 1.3 84.0 - - - +
184B CYS* 1.3 69.4 + - - +
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Residues in contact with CYS 184 (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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79B TRP* 4.0 20.9 - - + -
87B PHE* 3.2 5.2 - - - -
88B TYR* 2.9 41.0 + - + -
102B PHE* 3.9 8.7 - - - -
103B CYS* 2.1 52.5 - - + -
108B ALA* 4.2 1.1 - - + -
109B ASP 3.2 6.5 - - - +
111B ALA 4.3 0.2 - - - -
182B TRP* 3.6 15.0 - - - -
183B ILE* 1.3 79.8 - - - +
185B SER* 1.3 60.3 + - - +
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Residues in contact with SER 185 (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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79B TRP* 4.6 0.7 - - - -
85B LYS* 4.6 9.1 - - - -
86B CYS 3.1 6.7 - - - -
87B PHE* 3.6 30.1 - - - -
108B ALA* 3.4 2.8 - - - +
109B ASP* 2.9 33.7 + - - +
111B ALA* 3.5 4.8 - - - +
112B GLN* 3.1 32.6 + - - +
184B CYS* 1.3 74.0 - - - +
186B LYS* 1.3 63.5 + - - +
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Residues in contact with LYS 186 (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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76B PRO* 3.4 34.2 - - + +
79B TRP* 3.5 25.3 - - + -
85B LYS* 3.4 8.2 - - - +
86B CYS* 2.8 40.8 + - + -
106B GLN* 2.7 27.3 + - - +
107B ASP* 3.6 27.7 + - + +
108B ALA* 3.9 1.8 - - + -
185B SER* 1.3 76.7 - - - +
187B SER* 1.3 71.1 + - - +
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Residues in contact with SER 187 (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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84B ARG 3.5 8.2 + - - -
85B LYS* 4.4 5.7 - - - +
86B CYS* 4.4 0.3 - - - -
186B LYS* 1.3 88.5 - - - +
188B ASP* 1.3 71.2 + - - +
189B ILE* 3.7 1.6 + - - -
191B VAL* 4.0 24.5 - - - +
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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