Contacts of the strand formed by residues 154 - 164 (chain B) in PDB entry 1XPM
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 GLY 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43B ALA* 4.2 11.0 + - - -
140B THR 3.7 0.2 - - - -
141B ALA 2.8 28.0 + - - +
142B ARG* 5.4 0.5 - - - +
153B GLN* 1.3 78.5 - - - +
155B ALA* 1.3 63.1 + - - +
273B VAL 3.6 15.0 - - - -
274B GLY 4.3 0.2 - - - -
275B ASN 3.3 18.9 + - - -
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Residues in contact with ALA 155 (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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12B VAL* 3.8 5.4 - - - +
13B PRO* 3.4 23.0 - - + +
43B ALA* 3.8 14.3 - - + +
45B SER* 3.2 27.1 - - - +
54B MET* 4.4 6.1 - - - -
139B ASP 3.5 12.6 - - - +
140B THR* 4.1 11.2 - - + -
154B GLY* 1.3 75.9 - - - +
156B GLY* 1.3 59.2 + - - +
276B ILE* 3.4 14.1 - - - +
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Residues in contact with GLY 156 (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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11B TYR 3.2 13.7 - - - -
12B VAL* 4.4 3.6 - - - -
54B MET* 3.7 16.0 - - - +
138B THR* 3.6 0.7 - - - -
139B ASP 3.1 30.8 + - - +
155B ALA* 1.3 75.9 - - - +
157B ALA* 1.3 61.8 + - - +
276B ILE* 3.6 18.2 - - - +
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Residues in contact with ALA 157 (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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10B PHE* 3.1 5.5 - - - +
11B TYR 2.8 32.0 + - - +
54B MET* 3.5 33.7 - - + +
55B GLY* 3.8 5.4 - - - -
58B ALA* 3.6 4.5 - - + +
136B ILE* 4.7 0.4 - - + -
137B ALA 3.0 14.4 - - - +
138B THR* 3.7 11.0 - - - +
156B GLY* 1.3 76.0 - - - +
158B VAL* 1.3 65.8 + - - +
276B ILE* 4.5 3.1 - - - +
279B GLY* 6.0 0.2 - - - -
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Residues in contact with VAL 158 (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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8B ILE* 4.1 10.5 - - + -
9B ASN 3.3 11.2 - - - +
10B PHE* 3.9 11.9 - - + -
58B ALA* 4.3 1.1 - - - -
135B VAL 3.8 0.9 - - - +
136B ILE* 3.4 3.0 - - - -
137B ALA* 2.8 41.5 + - + +
157B ALA* 1.3 79.5 - - - +
159B ALA* 1.3 65.6 + - - +
160B MET* 4.4 5.5 - - + +
276B ILE* 4.0 11.2 - - + -
279B GLY* 3.6 24.2 - - - +
282B TYR* 3.8 22.0 - - + -
283B LEU* 4.0 8.7 - - - +
286B ILE* 4.1 12.8 - - + -
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Residues in contact with ALA 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ILE* 3.3 5.0 - - - +
9B ASN 2.8 32.0 + - - +
58B ALA* 3.7 9.3 - - + +
59B ALA* 3.6 43.1 - - + +
62B ILE* 3.6 7.8 - - + +
134B LEU* 4.4 2.0 - - + -
135B VAL 3.4 4.3 - - - -
136B ILE* 4.1 9.2 - - + -
158B VAL* 1.3 73.6 - - - +
160B MET* 1.3 64.3 + - - +
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Residues in contact with MET 160 (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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5B ILE* 4.0 21.5 - - + -
7B LYS 3.4 6.5 - - - +
8B ILE* 3.7 20.6 - - + -
114B ALA* 4.6 4.7 - - + -
118B ILE* 3.7 23.6 - - + -
133B VAL 3.6 0.7 - - - +
134B LEU* 3.6 3.6 - - - +
135B VAL* 2.8 52.0 + - + +
137B ALA* 5.6 1.6 - - + -
158B VAL* 4.4 8.3 - - + +
159B ALA* 1.3 80.2 - - - +
161B VAL* 1.3 63.9 + - - +
162B ILE* 3.9 12.5 + - + -
282B TYR* 3.5 49.8 - - + -
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Residues in contact with VAL 161 (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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5B ILE* 3.7 2.8 - - - -
6B ASP* 2.8 37.7 + - + +
7B LYS* 3.0 20.5 + - + +
62B ILE* 4.0 34.5 - - + +
63B ILE* 4.3 7.9 - - + -
67B ASP* 5.2 4.9 - - - +
71B ILE* 5.6 4.5 - - + -
132B LYS* 3.8 33.7 - - + +
133B VAL 3.5 5.8 - - - +
134B LEU* 4.2 14.1 - - + -
160B MET* 1.3 75.5 - - - +
162B ILE* 1.3 65.9 + - - +
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Residues in contact with ILE 162 (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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3B ILE* 4.0 13.0 - - + -
4B GLY* 3.2 16.4 - - - +
5B ILE* 3.9 21.3 - - + -
118B ILE* 4.0 24.2 - - + +
121B ALA* 4.1 26.9 - - + -
122B LYS* 4.3 6.7 - - + +
125B LEU* 3.5 17.4 - - + +
132B LYS* 3.3 5.0 - - - +
133B VAL* 2.8 38.2 + - + +
135B VAL* 4.3 10.8 - - + -
160B MET* 4.3 7.4 - - + +
161B VAL* 1.3 76.7 - - - +
163B ALA* 1.3 67.3 + - - +
171B LEU* 5.1 2.2 - - + -
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Residues in contact with ALA 163 (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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3B ILE* 4.0 6.5 - - - -
4B GLY 3.0 30.4 + - - +
6B ASP* 4.2 15.0 - - + -
125B LEU* 3.9 8.7 - - - -
131B GLU 4.4 2.5 - - - +
132B LYS* 3.7 33.0 - - + -
161B VAL 4.1 0.6 + - - -
162B ILE* 1.3 78.2 - - - +
164B HIS* 1.3 71.1 + - - +
166B PRO* 3.5 4.6 - - - +
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Residues in contact with HIS 164 (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 ALA 3.2 8.9 + - - +
3B ILE* 3.5 25.6 - - + +
6B ASP* 5.1 0.7 - - - +
125B LEU* 2.6 37.0 + - + -
126B ALA 4.0 10.1 - - - -
128B ARG 3.6 5.8 - - - -
129B PRO* 3.4 44.4 + - + +
131B GLU 4.7 3.5 + - - -
163B ALA* 1.3 81.3 - - - +
165B ASN* 1.3 74.3 + - - +
2C ALA 4.4 9.4 + - - -
129C PRO* 4.5 13.7 - - + +
164C HIS* 4.2 16.4 + - - +
165C ASN 5.3 4.0 - - - -
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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