Contacts of the strand formed by residues 132 - 141 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C ASP* 3.7 17.8 + - - -
7C LYS* 4.6 5.1 - - - +
67C ASP* 2.6 34.4 + - + +
70C LYS* 2.9 33.7 + - + +
71C ILE* 3.3 16.0 - - + -
72C GLY* 2.9 25.6 + - - -
125C LEU* 4.1 2.3 - - - +
130C ASN 5.5 0.2 - - - -
131C GLU* 1.3 80.1 - - - +
133C VAL* 1.3 68.3 + - - +
161C VAL* 3.8 18.6 - - + +
162C ILE 3.3 9.6 - - - +
163C ALA* 3.7 18.4 - - + -
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Residues in contact with VAL 133 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C ILE* 4.6 1.6 - - - -
73C MET* 3.6 33.2 - - + +
75C ILE* 4.4 3.8 - - + -
121C ALA* 3.6 28.0 - - + -
124C TYR* 3.7 30.5 - - + -
125C LEU* 3.9 11.7 - - + -
132C LYS* 1.3 81.3 - - - +
134C LEU* 1.3 71.0 + - - +
135C VAL* 3.9 6.6 + - + -
160C MET 3.6 1.2 - - - +
161C VAL* 3.5 4.5 - - - -
162C ILE* 2.8 36.4 + - + +
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Residues in contact with LEU 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C ALA* 4.1 16.4 - - + -
62C ILE* 5.3 0.2 - - + -
63C ILE* 4.2 9.2 - - + -
71C ILE* 4.1 16.0 - - + +
73C MET 3.0 12.2 + - - +
74C VAL* 3.4 11.0 - - + +
75C ILE 2.9 26.0 + - - +
96C LEU* 3.7 29.6 - - + -
98C ILE* 3.9 16.2 - - + -
133C VAL* 1.3 72.9 - - - +
135C VAL* 1.3 64.0 + - - +
136C ILE* 3.9 21.3 - - + -
159C ALA* 4.4 4.3 - - + -
160C MET 3.6 14.1 - - - +
161C VAL* 4.2 17.0 - - + +
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Residues in contact with VAL 135 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75C ILE* 3.4 9.6 - - + +
77C ALA* 5.6 1.1 - - + -
114C ALA* 4.3 6.5 - - + +
117C ALA* 3.7 44.9 - - + +
118C ILE* 3.9 26.7 - - + -
121C ALA* 4.4 2.0 - - + -
133C VAL* 4.1 14.4 - - + -
134C LEU* 1.3 76.7 - - - +
136C ILE* 1.3 69.8 + - - +
158C VAL 3.9 0.9 - - - +
159C ALA* 3.4 2.4 - - - -
160C MET* 2.8 51.8 + - + +
162C ILE* 4.4 4.3 - - + -
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Residues in contact with ILE 136 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C GLY* 3.7 37.0 - - - +
59C ALA* 4.0 4.0 - - + -
74C VAL* 4.9 4.5 - - + -
75C ILE 2.9 12.7 + - - +
76C VAL* 3.2 9.0 - - + +
77C ALA* 2.8 31.7 + - - +
92C ILE* 3.6 36.8 - - + -
134C LEU* 3.9 24.2 - - + -
135C VAL* 1.3 82.8 - - - +
137C ALA* 1.3 66.2 + - - +
138C THR* 4.3 6.7 - - + -
157C ALA* 4.7 1.3 - - + -
158C VAL 3.4 7.2 - - - +
159C ALA* 4.1 10.1 - - + -
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Residues in contact with ALA 137 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C ALA* 3.4 8.3 - - - -
114C ALA* 4.1 13.0 - - + -
135C VAL* 4.3 1.4 - - - +
136C ILE* 1.3 72.2 - - - +
138C THR* 1.3 58.7 + - - +
157C ALA* 3.0 6.1 - - - +
158C VAL* 2.8 39.2 + - + +
160C MET* 5.6 1.8 - - + +
278C THR* 3.3 22.4 - - - +
279C GLY* 3.6 24.9 - - - +
282C TYR* 5.4 1.3 - - + -
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Residues in contact with THR 138 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ILE* 2.8 48.4 + - + +
54C MET* 3.8 4.9 - - - +
55C GLY 4.0 0.2 + - - -
76C VAL* 3.7 28.0 - - + -
77C ALA 3.0 4.4 + - - -
78C THR* 2.7 31.6 + - - -
88C ALA* 5.7 0.2 - - + -
92C ILE* 5.3 1.8 - - + -
136C ILE* 4.3 8.5 - - + -
137C ALA* 1.3 75.3 - - - +
139C ASP* 1.3 62.8 + - - +
156C GLY 3.6 5.4 - - - -
157C ALA* 3.7 14.6 - - - +
276C ILE 5.0 0.4 - - - -
278C THR* 3.5 1.4 + - - -
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Residues in contact with ASP 139 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C ILE* 4.2 1.8 - - - -
54C MET* 3.6 4.9 - - - +
78C THR* 2.9 4.0 + - - -
79C GLU* 2.8 23.0 + - - +
80C SER* 2.5 25.7 + - - +
138C THR* 1.3 78.1 + - - +
140C THR* 1.3 63.2 + - - +
141C ALA 4.1 0.4 - - - -
155C ALA* 3.4 2.4 - - - -
156C GLY 3.1 31.7 + - - +
276C ILE* 3.4 19.8 + - - +
277C TYR* 3.4 16.5 - - + +
278C THR* 2.7 41.8 + - - +
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Residues in contact with THR 140 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C SER* 4.3 3.8 - - - +
49C GLN 5.5 0.7 - - - +
51C ILE* 4.6 8.7 - - + +
54C MET* 4.0 16.2 - - + -
80C SER* 3.1 23.1 + - - -
139C ASP* 1.3 79.3 - - - +
141C ALA* 1.3 60.5 + - - +
142C ARG* 3.2 30.4 + - - +
154C GLY 3.7 5.4 - - - -
155C ALA* 4.1 11.2 - - + -
277C TYR* 3.7 6.7 - - - -
353C PHE* 4.0 25.7 - - + -
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Residues in contact with ALA 141 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C ASP* 4.1 1.2 - - - +
140C THR* 1.3 67.8 - - - +
142C ARG* 1.3 61.1 + - - +
143C TYR* 4.2 5.2 - - + -
153C GLN* 3.3 26.9 - - - +
154C GLY 2.8 16.8 + - - +
275C ASN* 3.2 31.8 + - + +
277C TYR* 3.4 38.7 - - + +
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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