Contacts of the strand formed by residues 145 - 155 (chain C) in PDB entry 2AMT
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 145 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A LEU* 3.9 10.6 - - - +
10C HIS 3.2 14.1 - - - -
12C PHE* 3.5 16.0 - - - -
99C ILE 4.8 0.2 - - - +
100C ALA* 5.2 1.2 - - - -
139C PHE* 3.5 4.7 + - - -
140C THR* 3.6 24.7 - - - +
144C GLU* 1.3 81.2 - - - +
146C ILE* 1.3 68.3 + - - +
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Residues in contact with ILE 146 (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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9C VAL* 3.4 3.2 - - - -
10C HIS 3.1 30.9 + - - +
12C PHE* 3.5 30.3 - - + -
18C ILE* 3.8 24.2 - - + -
20C ILE* 4.1 8.1 - - + -
31C LEU* 4.4 6.1 - - + -
39C VAL* 3.3 26.5 - - + +
98C ILE* 3.9 9.9 - - + -
99C ILE 3.4 9.4 - - - +
100C ALA* 3.8 16.4 - - + -
102C ALA 4.3 2.7 - - - +
105C MET* 4.1 11.0 - - + -
139C PHE* 4.9 0.6 - - - -
140C THR* 4.2 1.3 - - - -
145C GLY* 1.3 79.2 - - - +
147C ALA* 1.3 74.0 + - - +
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Residues in contact with ALA 147 (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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7903A GPP 5.9 0.9 - - + -
7C PHE* 4.2 8.1 - - + -
8C ASP 3.3 5.6 - - - -
9C VAL* 3.8 19.5 - - + -
39C VAL* 4.7 0.2 - - - -
98C ILE* 3.7 0.3 - - - -
99C ILE* 2.7 57.9 + - + +
139C PHE* 4.7 2.5 - - + -
140C THR* 3.7 14.0 - - + +
146C ILE* 1.3 82.2 - - - +
148C CYS* 1.3 61.1 + - - +
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Residues in contact with CYS 148 (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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7C PHE* 3.3 7.7 - - - -
8C ASP 2.8 32.8 + - - +
39C VAL* 3.6 27.6 - - + +
40C ALA* 3.4 26.5 - - - +
43C ALA* 3.5 7.3 - - + +
96C VAL* 3.4 25.1 - - - -
97C THR 3.3 15.9 - - - -
98C ILE* 4.0 5.2 - - + -
99C ILE* 4.7 0.2 - - - -
147C ALA* 1.3 78.5 - - - +
149C GLU* 1.3 64.5 + - - +
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Residues in contact with GLU 149 (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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149A GLU* 2.6 23.0 - - - +
7903A GPP 3.6 6.8 - - - +
5B HIS* 3.0 36.2 + - + +
149B GLU* 3.4 11.1 - - - +
5C HIS* 2.8 24.5 + - - -
6C GLY 3.5 4.5 - - - -
7C PHE* 3.1 24.7 - - + -
96C VAL* 3.6 0.7 - - - -
97C THR* 2.6 41.6 + - - +
99C ILE* 3.7 20.4 - - + -
148C CYS* 1.3 77.9 - - - +
150C ALA* 1.3 60.1 + - - +
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Residues in contact with ALA 150 (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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5B HIS* 5.3 0.7 - - - -
5C HIS* 3.4 5.5 - - - -
6C GLY 2.7 34.6 + - - +
43C ALA* 3.5 34.3 - - + +
44C LEU* 3.7 11.7 - - + +
47C ALA* 3.9 3.4 - - + -
95C ASP 3.4 9.4 - - - +
96C VAL* 4.4 11.0 - - + -
149C GLU* 1.3 77.1 + - - +
151C VAL* 1.3 65.3 + - - +
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Residues in contact with VAL 151 (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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151A VAL* 4.8 5.4 - - + -
3B ILE* 3.6 31.1 - - + +
4B GLY 3.9 0.2 - - - -
5B HIS* 3.7 36.8 - - + +
151B VAL* 4.6 9.9 - - + -
3C ILE* 5.0 1.1 - - + -
4C GLY 3.2 9.9 - - - +
5C HIS* 4.1 17.3 - - + -
44C LEU* 5.1 0.5 - - - +
47C ALA* 4.2 2.5 - - - -
94C VAL* 3.5 4.0 - - - +
95C ASP* 2.9 49.9 + - + +
150C ALA* 1.3 80.1 - - - +
152C ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 152 (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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3B ILE* 3.8 4.0 - - - -
2C ARG 3.6 0.6 - - - +
3C ILE* 3.4 8.5 - - - +
4C GLY 2.9 30.5 + - - -
47C ALA* 3.9 24.9 - - + +
48C LEU* 3.8 29.8 - - + -
51C ALA* 4.7 4.5 - - + -
93C ASN 3.7 5.2 - - - -
94C VAL* 4.1 6.7 - - + -
151C VAL* 1.3 74.3 - - - +
153C LEU* 1.3 60.8 + - - +
154C LEU 4.2 0.2 - - - -
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Residues in contact with LEU 153 (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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153A LEU* 3.9 18.2 - - + -
1B MET* 3.3 39.3 - - + +
2B ARG 4.0 0.7 - - - -
3B ILE* 3.7 17.3 - - + +
153B LEU* 4.0 10.3 - - + -
1C MET* 4.5 13.9 - - + -
2C ARG 3.4 19.7 - - - +
3C ILE* 3.8 22.9 - - + -
91C LEU* 4.4 1.2 - - - +
92C GLY* 2.9 25.7 + - - -
93C ASN* 3.0 24.9 + - - +
152C ALA* 1.3 74.0 - - - +
154C LEU* 1.3 67.1 + - - +
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Residues in contact with LEU 154 (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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1C MET* 3.0 8.9 - - - +
2C ARG* 2.8 38.4 + - + +
48C LEU* 3.7 25.1 - - + +
51C ALA* 3.7 26.2 - - + -
52C ALA* 3.8 9.2 - - + +
81C TRP* 3.6 26.2 - - + -
84C ILE* 3.7 24.0 - - + -
89C TYR* 4.0 17.9 - - + -
90C THR 3.4 16.6 - - - +
91C LEU* 4.2 2.2 - - + -
153C LEU* 1.3 78.6 - - - +
155C ILE* 1.3 64.5 + - - +
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Residues in contact with ILE 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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1C MET* 4.2 34.5 - - + +
2C ARG* 6.5 0.2 - - - -
89C TYR* 3.2 10.2 - - - -
90C THR* 2.9 42.7 + - - +
91C LEU 3.7 20.4 - - - +
92C GLY* 3.8 15.0 - - - +
154C LEU* 1.3 78.3 - - - +
156C LYS* 1.3 76.1 + - - +
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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