Contacts of the strand formed by residues 184 - 189 (chain A) in PDB entry 4K81
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 184 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113A TYR* 3.8 39.9 - - + +
117A GLU* 2.8 26.9 + - - -
152A PHE 3.6 0.2 - - - +
153A GLU* 3.8 1.9 - - - -
154A HIS* 2.8 42.2 + - + +
156A PRO* 4.5 11.0 - - + -
177A TRP* 4.0 7.9 - - - -
182A GLU 3.8 10.5 - - - +
183A ASN* 1.3 81.8 - - - +
185A LEU* 1.3 60.9 + - - +
186A TYR* 2.9 34.3 + - + +
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Residues in contact with LEU 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ILE* 4.3 24.0 - - + -
111A LYS 3.8 18.8 + - - +
112A VAL* 3.7 8.7 - - + -
113A TYR* 2.8 31.7 + - - +
151A LEU* 4.1 21.1 - - + -
152A PHE 3.3 6.7 - - - +
153A GLU* 4.4 0.9 - - - -
164A ILE* 3.6 31.0 - - + -
170A VAL* 5.0 3.8 - - + -
173A VAL* 5.1 0.2 - - + -
174A LEU* 3.9 34.5 - - + -
177A TRP* 4.2 10.4 - - + -
184A LYS* 1.3 75.4 - - - +
186A TYR* 1.3 61.6 + - - +
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Residues in contact with TYR 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 4.1 2.5 - - - -
113A TYR* 3.2 15.5 - - + -
114A SER 3.4 31.0 - - - -
115A GLU* 4.5 4.7 - - - -
117A GLU* 2.7 33.5 + - - -
150A THR 3.5 0.2 - - - +
151A LEU* 3.4 8.0 - - - +
152A PHE* 2.9 45.5 + - + -
154A HIS* 3.5 51.0 - + + -
161A GLU* 5.8 0.9 - - - +
184A LYS* 2.9 31.9 + - + +
185A LEU* 1.3 76.8 - - - +
187A PHE* 1.3 61.8 + - - +
188A ARG* 4.1 10.3 - - + +
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Residues in contact with PHE 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 3.5 19.3 - - + -
113A TYR 2.9 13.5 + - - +
114A SER* 4.3 17.0 + - - +
115A GLU 4.9 0.5 + - - -
134A CYS* 3.9 30.5 - - - -
137A LEU* 3.8 34.1 - - + -
138A ILE* 4.1 4.9 - - + -
141A ASN* 4.2 6.7 - - - -
143A TYR* 3.9 17.5 - + - -
149A TRP* 3.5 52.2 - + + -
150A THR 3.4 14.4 - - - -
151A LEU* 4.6 2.2 - - + -
186A TYR* 1.3 75.4 - - - +
188A ARG* 1.3 63.9 - - - +
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Residues in contact with ARG 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A GLU* 4.0 27.8 - - + +
149A TRP* 3.7 15.9 - - - -
150A THR* 2.9 30.2 + - - +
152A PHE* 3.6 35.9 - - + -
161A GLU* 2.5 48.1 + - - -
186A TYR* 4.1 10.4 - - + +
187A PHE* 1.3 78.9 - - - +
189A LYS* 1.3 71.2 + - - +
190A ASN* 5.7 0.4 - - - +
26D ASN* 4.0 12.5 - - - +
149D ARG* 6.0 1.4 - - - +
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Residues in contact with LYS 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ASP* 3.8 12.3 - - - +
148A SER* 3.3 27.1 - - - +
149A TRP* 3.8 40.8 - - + +
188A ARG* 1.3 87.0 + - - +
190A ASN* 1.3 61.6 + - - +
191A TYR* 3.1 32.2 - - + +
25D GLN 4.2 9.7 + - - -
26D ASN* 3.3 39.8 + - - +
27D HIS* 4.3 9.0 - - - +
149D ARG* 5.9 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