Contacts of the strand formed by residues 158 - 163 (chain A) in PDB entry 1R18
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 TYR 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A ARG* 3.6 28.3 - - + +
82A ILE 3.9 13.5 - - - -
83A LEU* 3.9 28.2 - - + +
112A VAL* 4.5 6.4 - - + +
152A TYR* 2.6 41.2 + - - +
155A ASN* 3.0 33.9 - - + +
156A ALA* 3.7 8.3 - - - -
157A PRO* 1.3 74.5 - - - +
159A ASN* 1.3 64.4 + - - +
160A ALA 3.6 2.4 + - - +
161A ILE* 3.8 21.3 - - + -
177A GLN* 2.8 35.4 + - + +
178A LEU* 3.6 8.1 - - - +
179A ALA* 3.0 21.8 + - - -
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Residues in contact with ASN 159 (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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75A HIS* 3.6 17.9 - - + +
77A LYS* 6.2 0.9 - - + -
80A ALA* 3.1 23.3 - - + +
81A ARG* 2.9 34.8 + - - +
82A ILE* 5.5 0.2 - - + -
157A PRO 5.0 1.1 - - - +
158A TYR* 1.3 73.7 - - - +
160A ALA* 1.3 60.8 + - + +
179A ALA* 4.3 14.6 - - - +
180A SER 5.5 2.2 + - - -
181A GLY 6.4 0.6 - - - -
182A GLY* 3.1 11.9 - - - -
183A ARG 3.1 20.1 + - - -
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Residues in contact with ALA 160 (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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72A LEU* 4.4 19.3 - - + -
75A HIS* 4.0 22.4 - - + +
76A LEU* 5.0 1.6 - - + -
81A ARG 3.7 2.0 + - - -
82A ILE* 3.5 22.0 - - + -
83A LEU 3.1 22.0 + - - -
158A TYR* 3.2 2.7 - - - +
159A ASN* 1.3 82.8 - - - +
161A ILE* 1.3 67.4 + - - +
183A ARG 3.3 8.7 - - - +
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Residues in contact with ILE 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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72A LEU* 4.6 3.7 - - - +
83A LEU* 3.4 33.2 - - + +
85A VAL* 4.2 5.4 - - + -
158A TYR* 3.8 23.3 - - + -
160A ALA* 1.3 81.3 - - - +
162A HIS* 1.3 62.5 + - - +
163A VAL* 4.2 10.1 - - + -
174A LEU* 3.6 33.2 - - + +
177A GLN* 4.5 5.2 - - + +
178A LEU* 3.8 16.4 - - + -
183A ARG 2.9 8.6 + - - +
184A LEU* 3.3 20.8 - - + +
185A ILE* 2.9 28.6 + - - +
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Residues in contact with HIS 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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68A ALA* 3.9 21.0 - - + +
72A LEU* 4.2 9.6 - - + -
82A ILE* 5.6 0.4 - - - +
83A LEU 2.8 11.2 + - - +
84A ASP* 3.0 21.3 + - - +
85A VAL* 2.8 33.8 + - - +
92A LEU* 3.4 29.2 - - + +
96A PHE* 4.1 17.3 - + + -
161A ILE* 1.3 75.2 - - - +
163A VAL* 1.3 63.8 + - - +
164A GLY* 3.7 26.0 - - - -
185A ILE* 3.8 17.5 - - + +
197A MET* 5.0 4.6 - - + +
300A SAH 5.0 6.3 - - - -
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Residues in contact with VAL 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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85A VAL* 3.7 24.9 - - + -
161A ILE* 4.2 0.9 - - + -
162A HIS* 1.3 88.7 + - - +
164A GLY* 1.3 59.0 + - - +
165A ALA* 3.3 24.2 - - + +
167A ALA* 5.7 1.8 - - + -
174A LEU* 3.8 19.7 - - + -
184A LEU* 3.7 20.2 - - + -
185A ILE 2.9 20.1 + - - +
186A VAL* 3.7 17.3 - - + -
187A PRO* 3.3 20.4 - - - +
197A MET* 4.3 3.6 - - - +
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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