Contacts of the strand formed by residues 160 - 165 (chain A) in PDB entry 4UN7
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 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A TRP* 4.0 16.8 - - + -
129A ASN 3.9 10.8 - - - +
130A LYS* 4.1 3.6 - - + -
153A LEU* 3.9 2.6 - - - +
154A ASP* 3.0 6.4 + - - +
155A ASP* 2.9 37.6 + - + -
158A HIS* 3.7 22.9 - - + +
159A GLY* 1.3 75.9 - - - +
161A TYR* 1.3 73.7 + - - +
14C A 3.8 14.8 - - + -
15C C 3.8 42.6 - - + +
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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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128A TRP* 3.4 5.0 - - - -
129A ASN 3.0 35.5 + - - +
130A LYS 3.6 24.5 - - - -
132A LYS* 3.6 50.6 + - + +
135A LEU* 3.9 12.6 - - + -
151A ILE* 4.4 7.6 - - + -
152A HIS* 3.2 22.9 - - - +
153A LEU* 3.9 24.9 - - + +
154A ASP* 4.1 0.9 - - - +
159A GLY* 3.7 11.9 - - - -
160A VAL* 1.3 79.0 - - - +
162A VAL* 1.3 61.5 + - - +
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Residues in contact with VAL 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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126A ARG* 3.9 30.3 - - + -
127A ILE 3.3 10.1 - - - +
128A TRP* 3.6 21.1 - - + +
135A LEU* 4.1 3.6 - - - -
150A THR 3.8 0.3 - - - +
151A ILE* 3.3 6.6 - - - +
152A HIS* 2.9 41.1 + - + +
154A ASP* 3.7 27.3 - - + +
161A TYR* 1.3 76.0 - - - +
163A LEU* 1.3 64.5 + - - +
164A ASN* 4.5 9.2 - - + +
6B G 5.8 1.8 - - - +
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Residues in contact with LEU 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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125A LEU 3.8 0.3 - - - +
126A ARG* 3.5 3.1 - - - -
127A ILE* 2.8 42.8 + - + +
135A LEU* 3.4 43.9 - - + +
138A VAL* 3.8 21.3 - - + -
139A SER* 3.8 14.4 - - - +
142A LEU* 3.6 21.3 - - + -
149A ASN* 3.9 15.0 - - + +
150A THR 3.4 3.4 - - - +
151A ILE* 4.1 7.6 - - + -
162A VAL* 1.3 72.6 - - - +
164A ASN* 1.3 59.8 + - - +
165A ILE* 3.7 19.7 + - + +
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Residues in contact with ASN 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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124A ARG* 4.8 6.9 - - - +
125A LEU 3.6 4.9 - - - +
126A ARG* 3.4 26.5 - - + +
149A ASN* 3.1 5.2 - - - +
150A THR* 2.8 41.8 + - - +
152A HIS* 6.1 0.2 - - - +
162A VAL* 3.9 9.0 - - + -
163A LEU* 1.3 71.9 - - - +
165A ILE* 1.3 70.4 + - - +
166A SER* 3.8 1.5 + - - +
167A LEU* 6.2 0.2 - - - +
5B T 3.8 30.1 + - - +
6B G 3.6 26.6 + - - +
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Residues in contact with ILE 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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114A TYR* 4.5 0.2 - - + -
125A LEU* 2.8 51.5 + - + +
127A ILE* 4.1 14.8 - - + -
142A LEU* 4.1 11.9 - - + -
147A VAL* 3.8 20.6 - - + -
148A ARG 3.8 2.9 - - - -
149A ASN* 4.2 2.5 - - + -
163A LEU* 3.7 25.6 - - + +
164A ASN* 1.3 79.8 + - - +
166A SER* 1.3 77.4 + - - +
167A LEU* 3.3 6.2 + - - +
173A PHE* 3.8 38.8 - - + -
5B T 4.2 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