Contacts of the strand formed by residues 160 - 166 (chain A) in PDB entry 4P5K
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 PHE 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A CYS* 3.6 1.2 - - - -
124A ASN* 2.9 67.7 + - + +
125A GLY* 3.7 10.1 - - - -
158A GLU 5.7 1.1 - - - -
159A ASP* 1.3 74.8 - - - +
161A TYR* 1.3 70.5 + - - +
162A ASP* 4.1 14.6 - - - -
177A HIS* 3.4 38.6 - + + -
178A TRP 3.8 4.9 - - - +
179A GLU* 4.1 7.6 - - + +
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Residues in contact with TYR 161 (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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91A VAL* 6.5 0.4 - - - -
105A LEU* 3.9 19.7 - - + -
121A TRP* 4.9 3.8 - - + -
122A LEU 3.3 8.5 - - - +
123A CYS* 3.7 38.1 - - + -
151A LEU* 3.6 29.4 - - + -
153A PHE* 3.4 39.4 - + + +
154A VAL 4.3 8.0 + - - -
155A PRO* 5.9 1.3 - - + -
156A SER 5.8 1.8 - - - -
159A ASP* 4.2 26.5 + - + +
160A PHE* 1.3 74.3 - - - +
162A ASP* 1.3 70.2 + - - +
177A HIS* 3.6 1.4 - - - -
178A TRP* 2.9 55.2 + + + +
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Residues in contact with ASP 162 (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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121A TRP* 3.5 11.3 - - - -
122A LEU* 3.0 49.7 + - + +
125A GLY* 4.7 2.1 + - - -
160A PHE* 4.1 15.8 - - - -
161A TYR* 1.3 75.2 - - - +
163A CYS* 1.3 61.7 + - - +
164A ARG 3.6 1.0 + - - -
175A LEU* 4.0 28.1 - - + +
176A LYS 2.9 10.0 - - - +
177A HIS* 2.9 36.3 + - - +
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Residues in contact with CYS 163 (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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89A VAL* 4.5 5.3 - - + +
91A VAL* 3.9 15.0 - - + +
107A CYS* 2.0 53.2 - - + -
109A ILE* 4.3 1.6 - - - -
119A VAL* 3.7 25.8 - - - -
120A THR 4.0 2.9 - - - -
121A TRP* 4.4 12.1 - - + -
149A HIS* 5.3 0.2 - - - -
162A ASP* 1.3 71.4 - - - +
164A ARG* 1.3 58.8 + - - +
165A VAL* 4.1 6.3 - - - +
174A LEU 3.4 2.4 - - - +
175A LEU* 3.3 4.6 - - - -
176A LYS* 2.9 30.4 + - + +
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Residues in contact with ARG 164 (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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118A ASN 3.8 0.7 - - - +
119A VAL* 3.3 7.1 - - - +
120A THR* 2.9 55.0 + - - +
122A LEU* 4.4 18.1 - - + +
162A ASP 3.6 0.4 + - - -
163A CYS* 1.3 72.7 - - - +
165A VAL* 1.3 61.2 - - - +
166A GLU* 3.2 36.2 + - - +
173A PRO* 3.7 28.4 - - + +
174A LEU 3.4 2.5 - - - -
175A LEU* 3.9 33.0 - - + +
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Residues in contact with VAL 165 (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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87A PRO* 4.1 21.5 - - + -
89A VAL* 4.0 21.5 - - + -
109A ILE* 4.1 20.4 - - + -
117A LEU* 3.5 24.5 - - + -
118A ASN 3.5 4.0 - - - +
119A VAL* 4.3 8.3 - - + -
163A CYS* 4.3 11.0 - - - +
164A ARG* 1.3 77.8 - - - +
166A GLU* 1.3 69.0 + - - +
170A LEU* 4.1 2.3 - - + +
173A PRO* 3.4 6.8 - - - +
174A LEU* 2.7 45.7 + - + +
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Residues in contact with GLU 166 (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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117A LEU* 3.0 20.7 - - - +
118A ASN* 3.0 54.0 + - + +
164A ARG* 3.2 32.2 + - - +
165A VAL* 1.3 81.7 - - - +
167A HIS* 1.3 60.8 + - - +
170A LEU* 4.1 1.8 - - - -
173A PRO* 4.2 13.2 - - + +
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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