Contacts of the strand formed by residues 123 - 132 (chain B) in PDB entry 1XHU
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 123 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B TYR* 2.6 38.4 + + - -
80B PHE 5.2 4.7 + - - -
85B LEU* 3.4 40.7 - - + +
89B LEU* 4.2 9.2 - - + -
116B LEU* 4.4 4.3 - - + -
118B VAL* 3.3 36.2 - - + +
121B GLN* 3.1 27.4 - - - -
122B PHE* 1.3 77.6 - - - +
124B GLU* 1.3 54.0 + - - +
125B LEU* 3.9 8.3 - - + -
163B LEU* 2.8 12.0 + - + -
164B PHE* 2.7 21.0 - - + -
165B ASP* 2.5 34.5 + - - +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B SER* 2.5 20.1 + - - -
3B PHE* 2.9 43.0 + - + +
4B ILE* 3.7 14.0 + - - +
115B ILE 3.8 0.3 - - - +
116B LEU* 4.3 3.0 - - - +
117B LEU* 3.7 30.9 + - - +
122B PHE* 4.3 3.6 + - + -
123B TYR* 1.3 73.1 - - - +
125B LEU* 1.3 57.7 + - - +
126B LEU* 3.0 11.9 + - - +
165B ASP* 3.7 11.9 - - + -
167B ASN* 2.3 48.4 + - + +
187B PHE* 3.6 5.5 - - - -
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85B LEU* 4.6 2.5 - - + -
88B LEU* 3.8 19.1 - - + -
89B LEU* 3.7 20.4 - - + -
112B THR* 3.5 28.3 - - + -
113B ALA* 3.9 11.7 - - + -
115B ILE 3.8 6.1 - - - -
116B LEU* 3.8 20.6 - - + -
123B TYR* 4.0 7.9 - - + -
124B GLU* 1.3 67.2 - - - +
126B LEU* 1.3 62.1 + - - +
127B ASP* 5.2 0.9 - - - +
164B PHE* 3.9 22.4 - - + -
165B ASP 2.7 19.5 + - - +
166B ILE* 3.6 18.7 - - + +
167B ASN 3.3 21.9 + - - +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B ILE* 3.1 37.0 - - + -
41B VAL* 4.2 9.0 - - + -
45B LEU* 3.7 18.4 - - + -
113B ALA* 3.7 1.9 - - - +
114B ASP 3.1 6.9 + - - -
115B ILE* 2.8 58.1 + - + +
117B LEU* 4.5 2.5 - - + -
124B GLU* 3.0 8.8 + - - +
125B LEU* 1.3 73.3 - - - +
127B ASP* 1.3 75.1 + - - +
128B VAL* 4.7 4.7 - - + +
167B ASN* 3.8 10.3 - - + +
169B LEU* 4.1 13.0 - - + +
187B PHE* 4.0 19.1 - - + -
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Residues in contact with ASP 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B THR 5.0 11.0 - - - +
113B ALA* 5.6 0.4 - - - -
114B ASP* 3.2 20.1 - - - +
125B LEU 5.2 0.4 - - - +
126B LEU* 1.3 76.2 - - - +
128B VAL* 1.3 78.2 + - - +
129B LYS* 3.0 30.3 + - - -
142B ILE 3.6 4.5 - - - +
166B ILE* 6.3 0.2 - - + -
167B ASN 3.3 6.5 + - - +
168B TYR* 3.1 31.2 - - + -
169B LEU* 2.8 28.9 + - - +
7E C 5.5 4.6 - - - +
8F G 4.7 2.1 + - - -
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Residues in contact with VAL 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B GLU* 3.8 29.6 - - + +
41B VAL* 4.0 22.0 - - + -
114B ASP* 3.2 22.0 + - + +
115B ILE* 5.2 1.8 - - + -
126B LEU* 4.7 5.8 - - + -
127B ASP* 1.3 87.1 + - - +
129B LYS* 1.3 70.0 + - - +
130B THR* 4.4 5.3 + - + +
169B LEU* 3.3 26.5 - - + +
171B VAL* 3.5 25.6 - - + -
8F G 4.9 2.6 + - - +
9F A 4.4 4.7 + - - -
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B ASP* 3.0 26.9 + - - +
128B VAL* 1.3 74.6 - - - +
130B THR* 1.3 58.7 + - - +
140B PRO* 4.8 12.8 - - + -
141B ASN 2.6 29.4 + - - +
142B ILE* 2.8 47.4 + - + +
168B TYR* 4.6 8.3 - - + -
169B LEU 2.7 13.6 + - - +
170B GLU* 3.1 13.5 - - + +
171B VAL* 2.7 32.2 + - - -
212B VAL* 4.9 5.4 - - + -
7E C 6.4 3.1 - - - -
8F G 5.7 2.0 - - - -
9F A 3.2 22.7 - - - +
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Residues in contact with THR 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B ALA* 5.2 0.5 - - - +
34B GLY* 3.2 34.6 + - - +
35B GLU* 3.6 12.7 + - - -
37B PHE* 4.4 4.5 - - + -
128B VAL* 4.4 6.5 - - + -
129B LYS* 1.3 77.1 - - - +
131B ARG* 1.3 61.1 + - - +
140B PRO* 5.7 2.8 - - - +
171B VAL* 3.3 22.2 - - + -
173B TRP* 3.6 16.2 + - - -
9F A 3.0 37.1 + - - +
10F C 3.9 8.0 + - - -
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Residues in contact with ARG 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LYS 4.1 0.2 + - - -
130B THR* 1.3 76.3 - - - +
132B ASN* 1.3 69.2 + - - +
133B ILE* 3.1 22.5 + - - +
135B LYS 4.7 10.7 + - - -
136B SER* 5.4 2.2 - - - +
137B ALA* 4.8 8.9 + - + +
140B PRO* 6.1 0.9 - - + -
170B GLU* 3.6 13.7 + - + +
171B VAL 3.2 6.3 + - - -
172B ASP* 3.5 12.7 - - - +
173B TRP* 2.9 34.4 + - - -
211B HIS* 3.3 54.8 + - + +
213B ARG* 2.8 47.4 - - - +
214B ASP* 4.6 0.6 + - - -
10F C 3.6 14.8 - - - +
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Residues in contact with ASN 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU 6.0 1.1 - - - +
131B ARG* 1.3 74.3 - - - +
133B ILE* 1.3 62.3 + - - +
134B SER* 3.1 20.5 + - - -
135B LYS* 3.0 57.8 + - - +
137B ALA* 5.5 1.4 - - - +
173B TRP* 3.7 39.5 - - + +
174B GLU* 4.7 1.4 - - - -
175B LEU* 5.0 1.2 + - - +
10F C 2.9 25.0 + - - +
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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