Contacts of the strand formed by residues 145 - 155 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137D LEU* 4.1 6.2 - - - +
10F HIS 3.3 13.7 - - - -
11F ALA* 4.0 1.6 - - - -
12F PHE* 3.4 18.4 - - - -
99F ILE 4.8 0.2 - - - +
100F ALA* 5.1 1.2 - - - -
101F GLN 5.5 0.2 + - - -
139F PHE* 3.5 5.1 + - - -
140F THR* 3.6 25.5 - - - +
144F GLU* 1.3 80.6 - - - +
146F ILE* 1.3 69.0 + - - +
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Residues in contact with ILE 146 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 3.5 3.6 - - - -
10F HIS 2.9 32.1 + - - +
12F PHE* 3.6 29.8 - - + -
18F ILE* 3.8 24.0 - - + -
20F ILE* 4.1 8.3 - - + -
31F LEU* 4.4 5.4 - - + +
39F VAL* 3.3 27.1 - - + +
98F ILE* 3.9 10.1 - - + -
99F ILE 3.5 8.3 - - - +
100F ALA* 3.7 18.2 - - + -
102F ALA 4.2 2.0 - - - +
105F MET* 4.0 12.3 - - + -
139F PHE* 4.8 0.6 - - - -
140F THR* 4.3 1.1 - - - -
145F GLY* 1.3 78.8 - - - +
147F ALA* 1.3 74.0 + - - +
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Residues in contact with ALA 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8903D GPP 4.7 2.9 - - + -
7F PHE* 4.3 8.7 - - + -
8F ASP 3.4 5.4 - - - +
9F VAL* 3.9 18.6 - - + -
39F VAL* 4.7 0.2 - - - -
98F ILE 3.8 0.2 - - - -
99F ILE* 2.7 51.7 + - + +
139F PHE* 4.5 3.6 - - + -
140F THR* 3.6 18.6 - - + +
146F ILE* 1.3 81.9 - - - +
148F CYS* 1.3 59.2 + - - +
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Residues in contact with CYS 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F PHE* 3.4 5.9 - - - -
8F ASP 2.9 33.2 + - - +
39F VAL* 3.6 28.0 - - + +
40F ALA* 3.4 26.0 - - - +
43F ALA* 3.4 9.6 - - + +
96F VAL* 3.4 25.4 - - - -
97F THR 3.4 11.2 - - - -
98F ILE* 4.1 5.8 - - + -
99F ILE* 4.8 0.4 - - - -
147F ALA* 1.3 76.8 - - - +
149F GLU* 1.3 68.2 + - - +
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Residues in contact with GLU 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D GLU* 3.0 11.8 - - - +
8903D GPP 4.0 6.2 - - - +
5E HIS* 3.4 26.6 - - + +
7E PHE* 4.7 3.0 - - + -
149E GLU* 2.9 29.9 - - - +
5F HIS* 2.6 33.2 + - - -
6F GLY 3.6 0.9 - - - -
7F PHE* 3.4 15.5 - - + -
96F VAL* 3.6 0.2 - - - -
97F THR* 2.7 40.0 + - - +
99F ILE* 3.6 22.5 - - + +
148F CYS* 1.3 79.5 - - - +
150F ALA* 1.3 62.2 + - - +
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Residues in contact with ALA 150 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E HIS* 5.4 0.9 - - - -
5F HIS* 3.4 5.4 - - - -
6F GLY 2.7 33.9 + - - +
43F ALA* 3.4 32.8 - - + +
44F LEU* 3.7 12.6 - - + +
47F ALA* 3.9 3.6 - - + -
95F ASP 3.3 10.1 - - - +
96F VAL* 4.4 10.1 - - + -
149F GLU* 1.3 78.5 + - - +
151F VAL* 1.3 66.5 + - - +
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Residues in contact with VAL 151 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D VAL* 4.6 10.5 - - + -
3E ILE* 3.6 33.8 - - + +
4E GLY 3.9 1.1 - - - -
5E HIS* 3.5 45.5 - - + +
151E VAL* 4.7 2.0 - - + -
3F ILE* 5.1 0.2 - - + -
4F GLY 3.3 8.3 - - - +
5F HIS* 4.2 10.5 - - + -
44F LEU* 5.2 0.2 - - - +
47F ALA* 4.2 1.1 - - - -
93F ASN 4.2 0.2 - - - +
94F VAL* 3.4 4.9 - - - +
95F ASP* 2.9 48.9 + - + +
150F ALA* 1.3 80.2 - - - +
152F ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 152 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E ILE* 4.2 0.9 - - - -
2F ARG 3.6 0.9 - - - +
3F ILE* 3.3 8.8 - - - +
4F GLY 2.9 31.5 + - - -
44F LEU* 5.4 0.2 - - + -
47F ALA* 3.8 30.9 - - + +
48F LEU* 3.9 24.9 - - + -
51F ALA* 4.2 3.5 - - + +
93F ASN 3.7 3.8 - - - -
94F VAL* 4.0 6.1 - - + -
151F VAL* 1.3 76.8 - - - +
153F LEU* 1.3 62.3 + - - +
154F LEU* 4.0 0.7 - - + -
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Residues in contact with LEU 153 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D LEU* 4.2 18.6 - - + -
1E MET* 3.5 23.3 - - + +
2E ARG* 3.9 2.5 - - - -
3E ILE* 3.5 32.1 - - + +
153E LEU* 4.0 8.1 - - + -
1F MET* 3.7 19.3 - - + -
2F ARG 3.5 18.2 - - - +
3F ILE* 3.8 21.3 - - + -
91F LEU* 4.4 1.0 - - - +
92F GLY* 2.8 30.4 + - - -
93F ASN* 2.9 25.5 + - - +
94F VAL* 5.2 0.2 - - - +
152F ALA* 1.3 71.6 - - - +
154F LEU* 1.3 59.1 + - - +
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Residues in contact with LEU 154 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 3.2 9.0 - - - +
2F ARG* 2.9 35.4 + - + +
48F LEU* 3.6 29.6 - - + +
51F ALA* 3.6 26.0 - - + -
52F ALA 4.0 6.7 - - - +
81F TRP* 3.6 23.6 - - + -
84F ILE* 3.7 20.6 - - + -
89F TYR* 4.0 19.3 - - + -
90F THR 3.4 16.4 - - - +
91F LEU* 3.8 9.6 - - + -
152F ALA* 5.2 0.2 - - + -
153F LEU* 1.3 76.3 - - - +
155F ILE* 1.3 64.6 + - - +
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Residues in contact with ILE 155 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 3.6 31.6 - - + +
88F GLY 4.1 0.5 - - - +
89F TYR* 3.6 3.6 - - - -
90F THR* 3.0 41.7 + - - +
91F LEU 4.0 8.1 - - - +
92F GLY* 3.9 21.8 - - - +
154F LEU* 1.3 77.0 - - - +
156F LYS* 1.3 80.7 + - + +
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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