Contacts of the strand formed by residues 132 - 141 (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 LYS 132 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B ASP* 3.6 18.8 + - - -
67B ASP* 2.6 34.2 + - + +
70B LYS* 2.9 27.8 + - + +
71B ILE* 3.3 15.0 - - + -
72B GLY* 2.9 25.6 + - - -
124B TYR* 5.1 0.2 - - - -
125B LEU* 4.1 2.3 - - - +
130B ASN 5.3 0.4 - - - +
131B GLU* 1.3 80.1 - - - +
133B VAL* 1.3 68.4 + - - +
161B VAL* 3.8 20.3 - - + +
162B ILE 3.3 10.1 - - - +
163B ALA* 3.7 19.1 - - + -
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Residues in contact with VAL 133 (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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71B ILE* 4.5 1.6 - - - -
73B MET* 3.5 34.3 - - + +
75B ILE* 4.4 4.0 - - + -
121B ALA* 3.6 27.8 - - + -
124B TYR* 3.7 31.0 - - + -
125B LEU* 3.9 11.7 - - + -
132B LYS* 1.3 81.7 - - - +
134B LEU* 1.3 70.8 + - - +
135B VAL* 4.1 6.1 - - + -
160B MET 3.6 1.0 - - - +
161B VAL* 3.5 4.7 - - - +
162B ILE* 2.8 37.0 + - + +
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Residues in contact with LEU 134 (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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59B ALA* 4.1 17.3 - - + -
62B ILE* 5.3 0.2 - - + -
63B ILE* 4.6 8.5 - - + -
71B ILE* 4.1 16.2 - - + +
73B MET 3.0 12.0 + - - +
74B VAL* 3.3 11.2 - - + +
75B ILE 2.9 26.3 + - - +
96B LEU* 3.7 30.5 - - + -
98B ILE* 3.9 15.0 - - + -
133B VAL* 1.3 73.2 - - - +
135B VAL* 1.3 63.2 + - - +
136B ILE* 3.9 21.5 - - + -
159B ALA* 4.4 3.8 - - + -
160B MET 3.6 14.1 - - - +
161B VAL* 4.2 16.6 - - + +
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Residues in contact with VAL 135 (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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75B ILE* 3.4 9.9 - - + +
77B ALA* 5.5 0.7 - - + -
114B ALA* 4.3 8.3 - - + +
117B ALA* 3.7 41.3 - - + +
118B ILE* 3.8 31.4 - - + -
133B VAL* 4.1 14.6 - - + -
134B LEU* 1.3 77.6 - - - +
136B ILE* 1.3 69.1 + - - +
158B VAL 3.8 0.7 - - - +
159B ALA* 3.4 2.3 - - - -
160B MET* 2.8 46.1 + - + +
162B ILE* 4.3 6.7 - - + -
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Residues in contact with ILE 136 (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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55B GLY* 3.7 36.3 - - - +
59B ALA* 4.0 4.3 - - + -
74B VAL* 4.9 4.7 - - + -
75B ILE 2.9 13.1 + - - +
76B VAL* 3.3 8.3 - - + +
77B ALA* 2.7 32.2 + - - +
92B ILE* 3.6 37.0 - - + -
134B LEU* 3.9 24.2 - - + -
135B VAL* 1.3 83.3 - - - +
137B ALA* 1.3 66.2 + - - +
138B THR* 4.3 7.2 - - + -
157B ALA* 4.7 0.9 - - + -
158B VAL 3.4 6.5 - - - +
159B ALA* 4.1 10.3 - - + -
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Residues in contact with ALA 137 (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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77B ALA* 3.4 8.1 - - - -
114B ALA* 4.1 12.1 - - + -
135B VAL* 4.3 1.2 - - - +
136B ILE* 1.3 72.3 - - - +
138B THR* 1.3 58.5 + - - +
156B GLY 4.8 0.2 - - - -
157B ALA* 3.0 6.8 - - - +
158B VAL* 2.8 39.0 + - + +
160B MET* 5.6 2.2 - - + +
278B THR* 3.3 23.3 - - - +
279B GLY* 3.6 24.2 - - - +
282B TYR* 5.5 1.3 - - + -
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Residues in contact with THR 138 (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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51B ILE* 2.8 48.6 + - + +
54B MET* 3.8 5.4 - - - +
55B GLY 4.0 0.2 + - - -
76B VAL* 3.8 26.9 - - + -
77B ALA 3.0 4.4 + - - -
78B THR* 2.7 32.0 + - - -
88B ALA* 5.8 0.4 - - + -
92B ILE* 5.3 1.8 - - + -
136B ILE* 4.3 8.7 - - + -
137B ALA* 1.3 75.9 - - - +
139B ASP* 1.3 62.2 + - - +
156B GLY 3.6 5.2 - - - -
157B ALA* 3.7 14.1 - - - +
276B ILE 5.6 0.2 - - - -
278B THR* 3.5 1.4 + - - -
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Residues in contact with ASP 139 (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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51B ILE* 4.2 1.8 - - - -
54B MET* 3.5 4.9 - - - +
78B THR* 3.0 3.8 + - - -
79B GLU* 2.7 23.3 + - - +
80B SER* 2.6 24.9 + - - +
138B THR* 1.3 77.9 + - - +
140B THR* 1.3 64.1 + - - +
141B ALA 4.1 0.4 - - - -
155B ALA* 3.5 2.4 - - - -
156B GLY 3.1 31.3 + - - +
276B ILE* 3.4 19.4 + - - +
277B TYR* 3.3 16.9 - - + +
278B THR* 2.8 41.8 + - - +
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Residues in contact with THR 140 (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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45B SER* 4.4 4.0 - - - +
49B GLN 5.4 0.4 - - - +
51B ILE* 4.6 9.9 - - + +
54B MET* 4.0 16.6 - - + -
80B SER* 3.0 23.2 + - - -
139B ASP* 1.3 78.0 - - - +
141B ALA* 1.3 60.3 + - - +
142B ARG* 3.2 30.3 + - - +
154B GLY 3.7 4.9 - - - -
155B ALA* 4.1 10.1 - - + -
277B TYR* 3.6 6.7 - - - -
353B PHE* 4.0 25.3 - - + -
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Residues in contact with ALA 141 (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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139B ASP* 4.1 1.2 - - - +
140B THR* 1.3 68.5 - - - +
142B ARG* 1.3 61.9 + - - +
143B TYR* 4.2 4.7 - - + -
153B GLN* 3.3 26.7 - - - +
154B GLY 2.8 16.5 + - - +
275B ASN* 3.2 31.6 + - + +
277B TYR* 3.4 38.3 - - + +
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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