Contacts of the strand formed by residues 154 - 164 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43D ALA* 4.1 10.9 + - - -
140D THR* 3.8 0.2 - - - -
141D ALA 2.8 29.0 + - - +
142D ARG* 5.5 0.3 - - - +
153D GLN* 1.3 78.1 - - - +
155D ALA* 1.3 62.3 + - - +
273D VAL 3.6 14.6 - - - -
274D GLY 4.2 0.2 - - - -
275D ASN 3.2 18.3 + - - -
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Residues in contact with ALA 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D VAL* 3.8 6.1 - - - +
13D PRO* 3.3 24.0 - - + +
43D ALA* 3.8 14.6 - - + +
45D SER* 3.2 27.6 - - - +
54D MET* 4.5 5.4 - - - -
139D ASP 3.5 13.0 - - - +
140D THR* 4.1 9.6 - - + -
154D GLY* 1.3 76.1 - - - +
156D GLY* 1.3 58.8 + - - +
276D ILE* 3.5 14.1 - - - +
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Residues in contact with GLY 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D TYR 3.2 14.1 - - - -
12D VAL* 4.3 2.0 - - - -
54D MET* 3.7 15.7 - - - +
138D THR* 3.6 0.7 - - - -
139D ASP 3.1 30.7 + - - +
155D ALA* 1.3 76.8 - - - +
157D ALA* 1.3 62.1 + - - +
276D ILE* 3.6 17.7 - - - +
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Residues in contact with ALA 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D PHE* 3.1 5.5 - - - +
11D TYR 2.8 32.8 + - - +
54D MET* 3.5 33.4 - - + +
55D GLY* 3.8 5.4 - - - +
58D ALA* 3.6 3.1 - - + +
136D ILE* 4.6 0.7 - - + -
137D ALA 3.0 14.1 - - - +
138D THR* 3.8 11.4 - - - +
156D GLY* 1.3 75.0 - - - +
158D VAL* 1.3 66.3 + - - +
276D ILE* 4.5 3.1 - - - +
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Residues in contact with VAL 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ILE* 4.1 11.2 - - + -
9D ASN 3.3 10.8 - - - +
10D PHE* 3.9 11.4 - - + -
58D ALA* 4.3 1.6 - - - -
135D VAL 3.8 0.9 - - - +
136D ILE* 3.4 4.2 - - - +
137D ALA* 2.8 38.7 + - + +
157D ALA* 1.3 79.3 - - - +
159D ALA* 1.3 63.4 + - - +
160D MET* 4.4 5.1 - - + +
276D ILE* 4.1 9.6 - - + -
279D GLY* 3.6 24.5 - - - +
282D TYR* 3.8 23.6 - - + -
283D LEU* 3.9 10.5 - - - +
286D ILE* 4.1 11.9 - - + -
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Residues in contact with ALA 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ILE* 3.2 5.5 - - - +
9D ASN 2.8 34.2 + - - +
58D ALA* 3.6 28.9 - - + +
59D ALA* 3.6 23.8 - - + +
62D ILE* 3.6 7.0 - - + +
134D LEU* 4.5 2.0 - - + -
135D VAL 3.5 4.3 - - - -
136D ILE* 4.2 9.0 - - + -
158D VAL* 1.3 73.9 - - - +
160D MET* 1.3 63.8 + - - +
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Residues in contact with MET 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 4.0 21.3 - - + -
7D LYS 3.4 5.8 - - - +
8D ILE* 3.7 21.3 - - + -
114D ALA* 4.6 4.0 - - + -
118D ILE* 3.7 25.8 - - + -
133D VAL 3.6 0.7 - - - +
134D LEU* 3.6 5.1 - - - +
135D VAL* 2.9 47.7 + - + +
137D ALA* 5.7 2.0 - - + -
158D VAL* 4.4 7.9 - - + +
159D ALA* 1.3 79.4 - - - +
161D VAL* 1.3 63.4 + - - +
162D ILE* 3.9 13.5 + - + +
282D TYR* 3.5 49.8 - - + -
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Residues in contact with VAL 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D GLY 3.7 0.2 - - - +
5D ILE* 3.7 2.4 - - - -
6D ASP* 2.8 35.9 + - + +
7D LYS* 3.0 19.7 + - + +
62D ILE* 4.1 21.5 - - + +
63D ILE* 3.6 32.1 - - + -
67D ASP* 5.2 3.6 - - - +
71D ILE* 5.6 2.7 - - + -
132D LYS* 3.9 31.9 - - + +
133D VAL 3.4 8.1 - - - +
134D LEU* 4.1 5.6 - - + -
160D MET* 1.3 75.0 - - - +
162D ILE* 1.3 64.7 + - - +
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Residues in contact with ILE 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ILE* 4.1 11.7 - - + -
4D GLY* 3.2 14.4 - - - +
5D ILE* 3.9 26.7 - - + -
118D ILE* 3.9 31.0 - - + +
121D ALA* 4.1 27.6 - - + -
122D LYS* 4.3 6.5 - - + +
125D LEU* 3.5 13.4 - - + +
132D LYS* 3.3 5.2 - - - +
133D VAL* 2.8 39.5 + - + +
135D VAL* 4.4 5.8 - - + -
160D MET* 4.3 7.2 - - + +
161D VAL* 1.3 75.7 - - - +
163D ALA* 1.3 67.2 + - - +
171D LEU* 5.0 2.7 - - + -
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Residues in contact with ALA 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D ILE* 3.4 6.5 - - - -
4D GLY 2.9 32.1 + - - +
6D ASP* 4.2 16.6 - - + -
125D LEU* 3.8 8.7 - - - -
131D GLU 4.6 1.3 - - - +
132D LYS* 3.7 32.3 - - + -
161D VAL 4.0 0.6 + - - -
162D ILE* 1.3 78.4 - - - +
164D HIS* 1.3 69.9 + - - +
166D PRO* 3.5 3.7 - - - +
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Residues in contact with HIS 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B GLN* 6.1 2.5 - - + +
296B ALA* 4.1 15.3 + - - +
320B GLU* 4.3 7.6 + - - -
2D ALA 3.4 7.8 + - - +
3D ILE* 3.7 24.4 - - + +
6D ASP* 5.1 1.0 - - - +
125D LEU* 2.7 39.5 + - + +
126D ALA 4.3 5.4 - - - -
128D ARG 3.2 19.5 + - - -
129D PRO* 3.5 26.5 - - + +
131D GLU 4.3 5.6 + - - -
163D ALA* 1.3 80.9 - - - +
165D ASN* 1.3 85.7 + - - +
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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