Contacts of the strand formed by residues 174 - 180 (chain A) in PDB entry 1XKW
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 ALA 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A VAL* 3.8 22.9 - - + -
128A VAL* 3.6 24.4 - - + +
129A ASP 4.4 0.5 + - - -
130A SER* 3.6 13.3 + - - -
158A ILE* 4.0 16.4 - - + -
159A LEU 3.1 14.8 - - - +
160A ARG* 4.2 3.1 - - - -
161A GLY 4.1 4.4 + - - -
171A ASN 4.5 2.7 + - - +
173A ALA* 1.3 83.5 - - - +
175A THR* 1.3 63.6 + - - +
176A VAL* 4.1 1.8 - - + -
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Residues in contact with THR 175 (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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69A LEU* 5.0 6.4 - - + +
130A SER* 3.2 19.8 - - - +
132A GLU* 3.6 33.2 - - + +
157A GLU 3.6 1.4 - - - +
158A ILE* 3.3 5.2 - - - +
159A LEU* 2.9 37.7 + - + +
161A GLY 5.1 0.2 + - - -
163A ASN* 3.1 37.9 + - - +
167A HIS* 4.0 6.3 - - - +
174A ALA* 1.3 73.6 - - - +
176A VAL* 1.3 64.0 + - - +
177A ASN* 4.0 3.3 + - + +
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Residues in contact with VAL 176 (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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99A LEU* 4.7 8.5 - - + -
103A MET* 3.8 26.2 - - + -
128A VAL* 4.2 17.7 - - + -
130A SER 2.9 7.7 + - - -
131A PHE* 3.3 24.2 - - + +
132A GLU 2.8 26.7 + - - +
156A VAL* 3.8 25.8 - - + -
157A GLU 3.3 3.8 - - - +
158A ILE* 4.4 11.2 - - + -
174A ALA* 5.0 2.2 - - + -
175A THR* 1.3 77.6 - - - +
177A ASN* 1.3 60.8 + - - +
178A LEU* 3.9 14.4 - - + +
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Residues in contact with ASN 177 (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 THR* 4.2 4.2 + - - -
69A LEU* 3.9 20.1 - - + +
132A GLU* 3.4 22.2 - - - +
134A ASP 3.5 3.6 + - - -
135A GLY* 2.7 34.1 + - - +
155A ARG 4.0 0.2 - - - +
156A VAL* 3.6 2.9 - - - -
157A GLU* 2.8 72.6 + - + +
175A THR* 4.0 1.9 - - + -
176A VAL* 1.3 71.6 - - - +
178A LEU* 1.3 64.3 + - - +
179A VAL* 3.7 12.5 + - - +
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Residues in contact with LEU 178 (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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99A LEU* 4.0 22.9 - - + -
131A PHE* 5.8 1.6 - - + -
132A GLU 2.9 14.6 + - - +
133A LEU* 3.6 15.3 - - + -
134A ASP 3.0 22.0 + - - -
140A LEU* 4.3 16.8 - - + -
148A GLN* 5.6 4.5 - - + +
150A MET* 4.7 5.8 - - + -
153A TYR* 3.5 39.0 - - + +
155A ARG 3.9 2.9 - - - +
156A VAL* 3.9 35.9 - - + -
176A VAL* 3.9 13.9 - - + +
177A ASN* 1.3 69.0 + - - +
179A VAL* 1.3 62.7 + - - +
180A ARG* 3.7 1.9 + - - +
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Residues in contact with VAL 179 (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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60A ALA* 4.1 13.7 - - + -
68A THR* 4.4 3.8 - - - +
134A ASP* 3.5 10.5 - - - +
153A TYR* 3.4 5.2 - - - -
154A GLU* 2.7 35.4 + - + +
155A ARG* 3.1 45.5 + - + +
157A GLU* 3.8 23.3 - - + +
177A ASN* 3.7 25.6 - - - +
178A LEU* 1.3 70.3 - - - +
180A ARG* 1.3 63.0 + - - +
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Residues in contact with ARG 180 (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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60A ALA* 3.6 18.7 - - - +
133A LEU* 3.5 26.7 - - - +
134A ASP* 2.8 35.0 + - - +
152A ILE* 3.5 17.9 - - + +
153A TYR* 3.7 20.8 + - + -
154A GLU 4.1 0.9 - - - -
178A LEU 4.5 2.0 - - - +
179A VAL* 1.3 76.4 - - - +
181A LYS* 1.3 66.3 + - - +
182A ARG* 3.5 12.8 + - - +
243A TYR* 3.5 18.9 - - - +
261A GLN* 5.1 2.4 + - - +
304A ARG* 4.1 11.9 - - - +
306A PHE* 3.3 44.3 - - - -
324A GLU* 2.7 42.2 + - - -
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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