Contacts of the strand formed by residues 162 - 167 (chain A) in PDB entry 3SOQ
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 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A GLU* 2.9 36.1 + - - +
155A THR* 3.5 2.8 - - - -
156A ASP* 2.9 48.4 + - + +
160A VAL* 3.7 21.5 - - + +
161A PRO* 1.3 77.6 - - - +
163A ILE* 1.3 65.7 + - - +
164A GLU* 3.0 34.0 + - + +
173A ARG* 3.8 3.4 - - - +
175A ILE* 3.8 33.7 - - + +
177A ILE 3.3 14.1 - - - +
178A ASN* 4.7 2.9 - - + -
181A ILE* 3.7 8.9 - - - +
184A PRO* 4.0 0.5 - - - +
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Residues in contact with ILE 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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153A TYR* 5.2 0.4 - - + -
154A TRP 3.3 13.2 - - - +
155A THR* 4.2 10.8 - - + -
162A LYS* 1.3 77.7 - - - +
164A GLU* 1.3 67.5 + - - +
175A ILE* 3.7 3.8 - - - +
176A ILE* 2.9 43.3 + - + -
177A ILE* 2.9 26.4 + - + +
181A ILE* 3.7 11.9 - - + -
184A PRO* 4.5 0.4 - - + -
187A LEU* 4.3 11.2 - - + -
196A LEU* 4.1 9.6 - - + -
198A TRP* 3.4 56.8 - - + +
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Residues in contact with GLU 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A LEU* 4.2 0.3 - - - +
153A TYR* 3.3 6.2 - - - +
154A TRP* 3.0 60.5 + - + +
162A LYS* 3.0 38.1 + - + -
163A ILE* 1.3 81.5 - - - +
165A ARG* 1.3 63.4 + - - +
173A ARG* 2.8 51.7 + - - +
174A PHE* 3.5 9.4 - - - +
175A ILE* 3.8 16.1 - - + +
176A ILE* 4.3 4.0 - - - +
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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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151A PHE* 3.7 41.2 - - + -
152A MET 3.1 13.9 - - - +
153A TYR* 3.4 36.5 + - + -
154A TRP* 4.3 3.6 - - - -
164A GLU* 1.3 75.4 - - - +
166A ALA* 1.3 65.4 + - - +
172A SER 3.6 1.6 - - - +
173A ARG* 3.4 1.2 - - - +
174A PHE* 2.9 60.2 + - + -
176A ILE* 4.2 6.0 - - + +
211A LEU* 3.1 31.5 + - - +
212A ASP* 3.9 16.8 - - - +
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Residues in contact with ALA 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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133A PHE* 3.6 32.8 - - + -
151A PHE* 3.4 10.5 - - - -
152A MET* 2.8 30.3 + - + +
154A TRP* 3.8 8.7 - - + -
165A ARG* 1.3 79.4 - - - +
167A GLY* 1.3 64.8 + - - +
171A SER 3.4 13.0 - - - +
172A SER 3.6 5.8 - - - -
173A ARG* 3.8 5.8 - - - -
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Residues in contact with GLY 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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150A GLY 3.3 10.8 - - - -
151A PHE* 4.2 2.0 - - - -
152A MET* 3.1 11.5 - - - +
166A ALA* 1.3 75.4 - - - +
168A MET* 1.3 59.0 + - - -
169A ASP* 2.8 20.2 - - - -
170A GLY* 2.9 16.1 + - - -
171A SER* 2.7 15.2 + - - -
172A SER 4.4 1.0 + - - -
301A PRO* 3.5 15.6 - - - +
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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