Contacts of the strand formed by residues 162 - 167 (chain A) in PDB entry 2UZ3
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 HIS 162 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PRO* 3.7 8.6 - - - +
126A LYS* 3.7 35.1 - - + -
130A GLY* 4.0 13.7 + - - -
160A ALA 3.6 0.6 - - - -
161A THR* 1.3 107.8 + - - +
163A SER* 1.3 59.0 + - - +
189A ALA* 3.4 6.1 - - - +
190A VAL* 2.8 35.0 + - + +
192A ARG* 3.9 41.3 + - + +
195A HIS* 3.6 39.2 - + + +
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Residues in contact with SER 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A PRO* 3.8 4.9 - - - +
21A MET* 3.0 41.6 + - - +
124A LEU* 4.0 4.0 - - - +
126A LYS* 4.8 8.8 + - - +
127A ASN 4.3 2.8 + - - +
128A PHE* 3.7 12.4 - - - +
162A HIS* 1.3 72.0 - - - +
164A LEU* 1.3 59.2 + - - +
187A TYR* 4.9 1.3 - - - -
188A SER 3.5 6.7 - - - -
189A ALA* 4.7 0.2 - - - +
195A HIS* 3.0 19.7 + - - -
1220A TTP 3.5 27.4 - - - -
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Residues in contact with LEU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A GLU* 6.1 2.2 - - + -
162A HIS 4.0 0.4 + - - -
163A SER* 1.3 73.9 - - - +
165A ARG* 1.3 66.9 + - - +
166A LYS* 3.8 30.4 + - + +
171A HIS* 4.2 11.9 - - + +
186A PHE 3.7 0.3 - - - +
187A TYR* 3.3 8.3 - - - +
188A SER* 2.8 53.3 + - - +
190A VAL* 3.8 25.8 - - + -
194A HIS 4.0 8.5 - - - +
195A HIS* 3.8 12.3 - - + +
196A LYS 3.8 35.4 - - - +
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Residues in contact with ARG 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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128A PHE* 3.4 34.3 + - + +
163A SER 4.3 1.2 + - - -
164A LEU* 1.3 79.8 - - - +
166A LYS* 1.3 65.3 + - - +
167A ILE* 4.2 9.6 - - + -
171A HIS* 3.6 5.5 - - - +
172A ALA* 2.9 41.5 + - + +
176A ASP* 3.9 20.0 + - - +
177A ASP* 2.9 30.3 + - - +
178A ILE 3.0 16.8 + - - -
180A LYS* 3.6 27.9 - - - +
186A PHE* 3.4 15.9 - - + +
187A TYR* 3.4 34.6 + - + -
1220A TTP 4.0 0.6 + - - -
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Residues in contact with LYS 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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154A ASN* 6.0 0.2 + - - -
155A GLU* 5.8 8.1 - - - +
164A LEU* 3.8 21.2 + - + +
165A ARG* 1.3 75.8 - - - +
167A ILE* 1.3 71.7 + - - +
169A GLY* 4.1 19.7 - - - +
170A LYS 3.0 17.5 - - - +
171A HIS* 3.4 33.6 + - + -
185A GLU 4.0 5.5 - - - +
186A PHE* 2.9 26.1 + - - +
188A SER* 5.5 3.5 + - - +
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Residues in contact with ILE 167 (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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165A ARG* 4.2 17.7 - - + -
166A LYS* 1.3 83.4 - - - +
168A ASP* 1.3 76.6 + - - +
169A GLY 3.1 0.2 - - - -
170A LYS* 2.8 34.3 + - - +
172A ALA* 4.9 8.3 - - + +
176A ASP* 5.8 1.8 - - - +
180A LYS* 4.1 20.6 - - - +
185A GLU 5.8 0.2 - - - -
186A PHE* 3.9 27.4 - - + -
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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