Contacts of the strand formed by residues 154 - 164 (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 GLY 154 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C ALA* 4.1 11.4 + - - -
140C THR 3.7 0.3 - - - -
141C ALA 2.8 27.7 + - - +
142C ARG* 5.5 0.2 - - - +
153C GLN* 1.3 78.3 - - - +
155C ALA* 1.3 63.0 + - - +
273C VAL 3.6 15.5 - - - -
274C GLY 4.3 0.2 - - - -
275C ASN 3.3 18.0 + - - -
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Residues in contact with ALA 155 (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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12C VAL* 3.8 8.1 - - - +
13C PRO* 3.4 23.0 - - + +
43C ALA* 3.8 12.4 - - + +
45C SER* 3.2 27.4 - - - +
54C MET* 4.4 6.3 - - - -
139C ASP 3.4 12.1 - - - +
140C THR* 4.1 11.0 - - + -
154C GLY* 1.3 75.9 - - - +
156C GLY* 1.3 58.3 + - - +
276C ILE* 3.4 13.6 - - - +
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Residues in contact with GLY 156 (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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11C TYR 3.2 13.7 - - - -
12C VAL* 4.3 3.8 - - - -
54C MET* 3.8 15.3 - - - +
137C ALA 4.8 0.2 - - - -
138C THR* 3.6 0.5 - - - -
139C ASP 3.1 30.9 + - - +
155C ALA* 1.3 76.4 - - - +
157C ALA* 1.3 61.5 + - - +
276C ILE* 3.6 18.4 - - - +
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Residues in contact with ALA 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C PHE* 3.1 5.5 - - - +
11C TYR 2.9 33.0 + - - +
54C MET* 3.6 33.4 - - + +
55C GLY* 3.9 5.2 - - - +
58C ALA* 3.7 4.3 - - + +
136C ILE* 4.7 0.7 - - + -
137C ALA 3.0 14.1 - - - +
138C THR* 3.7 11.4 - - - +
156C GLY* 1.3 75.8 - - - +
158C VAL* 1.3 65.4 + - - +
276C ILE* 4.5 3.1 - - - +
279C GLY* 6.0 0.2 - - - -
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Residues in contact with VAL 158 (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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8C ILE* 4.2 10.5 - - + -
9C ASN 3.3 11.0 - - - +
10C PHE* 3.9 12.3 - - + -
58C ALA* 4.3 1.1 - - - -
135C VAL 3.9 0.9 - - - +
136C ILE* 3.4 2.8 - - - -
137C ALA* 2.8 38.6 + - + +
157C ALA* 1.3 79.9 - - - +
159C ALA* 1.3 65.6 + - - +
160C MET* 4.5 5.5 - - + +
276C ILE* 4.0 11.0 - - + -
279C GLY* 3.6 24.5 - - - +
282C TYR* 3.8 23.3 - - + -
283C LEU* 4.0 9.0 - - - +
286C ILE* 4.1 13.0 - - + -
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Residues in contact with ALA 159 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.3 5.4 - - - +
9C ASN 2.8 34.6 + - - +
58C ALA* 3.7 10.2 - - + +
59C ALA* 3.6 42.2 - - + +
62C ILE* 3.6 7.8 - - + +
134C LEU* 4.4 2.0 - - + -
135C VAL 3.4 4.0 - - - -
136C ILE* 4.1 9.2 - - + -
158C VAL* 1.3 73.1 - - - +
160C MET* 1.3 64.0 + - - +
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Residues in contact with MET 160 (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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5C ILE* 4.0 21.8 - - + -
7C LYS 3.4 6.3 - - - +
8C ILE* 3.7 20.9 - - + -
114C ALA* 4.6 5.2 - - + -
118C ILE* 3.7 23.1 - - + -
133C VAL 3.6 1.2 - - - +
134C LEU* 3.6 3.6 - - - +
135C VAL* 2.8 52.0 + - + +
137C ALA* 5.6 1.8 - - + -
158C VAL* 4.5 8.1 - - + +
159C ALA* 1.3 80.4 - - - +
161C VAL* 1.3 63.4 + - - +
162C ILE* 3.9 12.5 + - + -
282C TYR* 3.5 49.4 - - + -
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Residues in contact with VAL 161 (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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5C ILE* 3.7 2.6 - - - -
6C ASP* 2.8 38.1 + - + +
7C LYS* 3.0 22.1 + - + +
62C ILE* 4.0 24.5 - - + +
63C ILE* 3.7 30.1 - - + -
67C ASP* 5.3 2.9 - - - +
71C ILE* 5.7 1.8 - - + -
132C LYS* 3.8 33.0 - - + +
133C VAL 3.5 6.1 - - - +
134C LEU* 4.2 5.8 - - + -
160C MET* 1.3 74.6 - - - +
162C ILE* 1.3 65.8 + - - +
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Residues in contact with ILE 162 (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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3C ILE* 4.0 12.6 - - + -
4C GLY* 3.2 17.0 - - - +
5C ILE* 3.9 22.7 - - + -
118C ILE* 4.0 29.4 - - + +
121C ALA* 4.1 25.6 - - + -
122C LYS* 4.3 6.7 - - + +
125C LEU* 3.5 17.9 - - + +
132C LYS* 3.3 5.2 - - - +
133C VAL* 2.8 37.9 + - + +
135C VAL* 4.4 5.2 - - + -
160C MET* 4.4 7.4 - - + +
161C VAL* 1.3 76.2 - - - +
163C ALA* 1.3 67.8 + - - +
171C LEU* 5.0 2.5 - - + -
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Residues in contact with ALA 163 (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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3C ILE* 3.3 6.2 - - - -
4C GLY 2.9 31.5 + - - +
6C ASP* 4.2 15.7 - - + +
125C LEU* 3.9 8.7 - - - -
131C GLU 4.4 2.9 - - - +
132C LYS* 3.7 32.5 - - + -
161C VAL 4.1 0.6 + - - -
162C ILE* 1.3 78.1 - - - +
164C HIS* 1.3 71.5 + - - +
166C PRO* 3.5 4.3 - - - +
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Residues in contact with HIS 164 (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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2B ALA 4.3 9.6 + - - -
129B PRO* 4.6 13.7 - - + +
164B HIS* 4.2 16.4 + - - +
165B ASN 5.3 4.0 - - - -
2C ALA 3.3 9.1 + - - +
3C ILE* 3.6 26.0 - - + +
6C ASP* 5.1 0.7 - - - +
125C LEU* 2.6 36.0 + - + -
126C ALA 4.0 10.1 - - - -
128C ARG 3.7 5.8 - - - -
129C PRO* 3.4 43.7 + - + +
131C GLU 4.7 3.7 + - - -
163C ALA* 1.3 81.5 - - - +
165C ASN* 1.3 74.7 + - - +
166C PRO 3.2 0.4 - - - -
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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