Contacts of the strand formed by residues 159 - 165 (chain A) in PDB entry 1XRE
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 ILE 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136A VAL* 3.2 4.0 - - - -
137A LEU* 2.8 52.2 + - + +
154A LEU* 5.0 2.9 - - + -
157A GLY 4.9 4.5 - - - +
158A LYS* 1.3 73.8 - - - +
160A PRO* 1.3 77.1 - - + +
161A LEU* 3.5 3.2 + - + +
198A LYS 5.3 1.1 - - - +
202A ALA* 3.8 46.9 - - + +
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Residues in contact with PRO 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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81A TYR* 3.3 29.4 + - + +
85A LEU* 3.8 11.7 - - + +
134A TRP* 3.7 36.8 - - + -
135A LEU 3.7 6.5 - - - +
136A VAL* 4.2 2.0 - - + -
153A PRO* 4.0 15.7 - - + -
154A LEU* 3.6 10.3 - - + -
158A LYS 3.5 9.2 - - - +
159A ILE* 1.3 91.2 - - + +
161A LEU* 1.3 66.2 + - - +
162A LEU 4.9 0.2 - - - +
198A LYS* 4.5 10.4 - - - +
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Residues in contact with LEU 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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85A LEU* 4.8 4.7 - - - -
89A VAL* 3.9 9.9 - - - +
102A VAL* 4.8 4.7 - - + -
135A LEU* 2.9 20.4 + - + +
136A VAL 4.5 1.6 - - - -
137A LEU* 4.4 7.4 - - + +
142A LEU* 3.8 31.6 - - + -
159A ILE* 3.9 11.2 - - + +
160A PRO* 1.3 83.1 - - - +
162A LEU* 1.3 60.7 + - - +
195A VAL* 3.8 32.2 - - + +
198A LYS* 3.8 31.5 - - + +
199A TYR* 3.9 25.1 - - + -
202A ALA* 4.2 11.2 - - + -
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Residues in contact with LEU 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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85A LEU* 4.6 3.7 - - - +
89A VAL* 3.8 28.3 - - + -
116A LEU* 5.7 1.6 - - + -
120A LEU* 3.9 23.1 - - + -
134A TRP* 3.5 5.9 - - - -
135A LEU* 2.9 45.7 + - + +
160A PRO 3.8 0.8 - - - -
161A LEU* 1.3 79.4 - - - +
163A VAL* 1.3 66.7 + - - +
186A TRP* 3.8 26.0 - - + -
187A TRP* 4.4 4.7 - - + -
190A VAL* 4.1 9.0 - - + -
192A TRP* 4.0 28.5 - - + -
195A VAL* 3.9 13.5 - - + -
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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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82A CYS 4.0 7.0 - - - +
85A LEU* 3.8 15.3 - - + -
86A PHE* 3.5 41.8 - - + +
89A VAL* 4.0 5.2 - - + +
120A LEU* 6.0 0.9 - - - -
132A TYR* 3.5 28.5 - - + -
133A GLY 3.3 13.2 - - - +
134A TRP* 3.6 32.3 - - + -
162A LEU* 1.3 76.6 - - - +
164A ILE* 1.3 62.3 + - - +
186A TRP* 3.3 19.8 - - - -
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Residues in contact with ILE 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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86A PHE* 4.1 2.7 - - - -
120A LEU* 4.8 9.6 - - + +
124A ALA* 3.8 22.7 - - + -
132A TYR* 3.2 9.5 - - - -
133A GLY* 2.9 43.7 + - - +
163A VAL* 1.3 74.1 - - - +
165A ASP* 1.3 70.6 + - - +
166A VAL* 3.6 2.9 + - + +
182A PHE* 4.1 9.2 - - + -
183A VAL* 4.0 31.2 - - + -
186A TRP* 3.6 55.4 - - + +
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Residues in contact with ASP 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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28A HIS* 2.8 10.6 + - - -
83A HIS* 3.3 3.8 + - - -
86A PHE* 3.7 28.3 - - + -
131A GLY 3.8 0.3 - - - +
132A TYR* 3.5 22.3 - - + -
164A ILE* 1.3 70.8 - - - +
166A VAL* 1.3 59.5 + - - +
167A TRP* 2.9 38.1 + - - +
170A ALA* 3.5 10.4 - - + +
182A PHE* 3.4 24.8 - - - -
209A MN 1.9 36.1 + - - -
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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