Contacts of the strand formed by residues 166 - 174 (chain L) in PDB entry 4R2G
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 166 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3L VAL 4.1 14.1 - - - +
4L VAL* 3.3 21.5 - - + +
5L LEU* 3.0 59.6 + - + +
161L VAL 3.7 0.9 - - - +
162L LEU* 3.7 1.2 - - - +
163L GLN* 2.9 34.8 + - - +
164L ASN 2.9 7.1 + - - +
165L GLN* 1.3 81.4 - - - +
167L LYS* 1.3 75.5 + - - +
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Residues in contact with LYS 167 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5L LEU* 3.8 5.1 - - - +
131L ARG* 5.9 2.6 - - - +
160L THR* 3.7 24.1 - - + +
161L VAL 3.1 6.7 - - - +
162L LEU* 3.8 36.0 - - + +
165L GLN 5.8 0.7 - - - -
166L LYS* 1.3 91.6 - - - +
168L VAL* 1.3 62.5 + - - +
169L GLU* 6.0 0.9 - - + -
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Residues in contact with VAL 168 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5L LEU* 3.6 22.9 - - + +
6L GLY* 4.9 2.5 - - - -
7L LYS* 3.5 34.3 - - + +
98L PHE* 5.0 9.9 - - + -
159L CYS 3.7 1.0 - - - +
160L THR* 3.5 2.8 - - - -
161L VAL* 2.9 47.1 + - + +
167L LYS* 1.3 76.0 - - - +
169L GLU* 1.3 67.3 + - - +
170L PHE* 3.4 22.2 + - + -
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Residues in contact with GLU 169 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L LYS* 3.2 24.8 + - - +
131L ARG* 5.8 1.7 + - - -
158L THR* 3.7 23.8 - - + +
159L CYS 3.5 2.9 - - - +
160L THR* 3.3 30.0 + - + +
167L LYS* 5.9 0.9 - - + -
168L VAL* 1.3 80.7 - - - +
170L PHE* 1.3 61.8 + - - +
171L LYS* 5.2 5.2 - - + +
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Residues in contact with PHE 170 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7L LYS* 3.6 33.9 - - + +
8L LYS 4.6 1.8 - - - -
98L PHE* 2.8 39.3 - - + -
99L GLY* 3.9 3.1 - - - -
100L LEU* 3.7 45.3 - - + -
157L TRP 3.6 1.4 - - - +
158L THR* 3.8 1.7 - - - +
159L CYS* 2.9 36.0 + - - +
161L VAL* 3.8 24.0 - - + -
168L VAL* 3.4 25.8 - - + -
169L GLU* 1.3 75.7 - - - +
171L LYS* 1.3 62.8 + - - +
172L ILE* 4.0 3.7 + - + -
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Residues in contact with LYS 171 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7L LYS* 4.4 8.0 - - - +
156L THR* 3.5 30.1 + - + +
157L TRP 3.3 4.7 - - - +
158L THR* 3.7 28.9 + - + -
169L GLU* 5.2 5.6 - - + +
170L PHE* 1.3 76.7 - - - +
172L ILE* 1.3 62.6 + - - +
173L ASP* 4.3 2.7 + - - +
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Residues in contact with ILE 172 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100L LEU* 3.3 35.9 - - + -
101L THR 4.3 8.3 - - - +
102L ALA* 5.3 8.5 - - + -
116L LEU* 3.6 28.7 - - + -
155L GLY 3.4 4.2 - - - +
156L THR* 3.4 2.2 - - - +
157L TRP* 2.9 46.5 + - + +
159L CYS* 4.2 8.3 - - - -
170L PHE* 4.6 3.8 - - + +
171L LYS* 1.3 79.5 - - - +
173L ASP* 1.3 72.8 + - - +
174L ILE* 3.7 6.6 + - + +
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Residues in contact with ASP 173 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106L THR* 4.4 10.2 - - - +
155L GLY 3.6 3.4 - - - +
156L THR* 3.4 26.3 + - - +
171L LYS 4.3 2.0 + - - -
172L ILE* 1.3 81.2 - - - +
174L ILE* 1.3 60.8 + - - +
175L VAL* 5.5 1.2 - - - +
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Residues in contact with ILE 174 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105L ASP 4.7 3.4 - - - +
106L THR* 3.2 22.0 - - - +
108L LEU* 3.7 24.7 - - + -
114L LEU* 4.6 20.2 - - + -
149L LEU* 4.5 16.4 - - + -
153L ASP 4.4 2.0 - - - +
154L SER* 3.5 4.3 - - - -
155L GLY* 2.9 40.1 + - - +
157L TRP* 3.3 39.9 - - + +
172L ILE* 4.7 7.4 - - + +
173L ASP* 1.3 76.8 - - - +
175L VAL* 1.3 70.5 + - - +
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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