Contacts of the strand formed by residues 2 - 11 (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 ARG 2 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D GLY 4.5 2.1 + - - +
93D ASN* 3.4 31.2 - - + +
94D VAL 5.4 1.2 + - - -
125D ASP* 2.6 29.5 + - - -
126D ASP* 3.0 32.3 + - - +
128D ASN 5.5 0.2 - - - +
153D LEU* 4.0 0.7 - - - -
1F MET* 1.3 80.3 - - - +
3F ILE* 1.3 60.4 - - - +
50F GLY 4.6 0.8 + - - -
51F ALA* 2.6 34.8 + - + +
53F ALA* 3.5 15.2 - - - +
89F TYR* 3.4 36.2 + - + -
152F ALA 3.6 1.0 - - - +
153F LEU* 3.4 9.6 - - - -
154F LEU* 2.9 38.0 + - + +
156F LYS 5.4 2.0 - - - +
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Residues in contact with ILE 3 (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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3D ILE* 3.6 16.4 - - + -
93D ASN* 2.8 54.5 + - - +
94D VAL* 5.0 0.7 - - - -
95D ASP* 3.9 5.5 - - - +
151D VAL* 3.7 24.0 - - + +
152D ALA* 4.0 5.2 - - - -
153D LEU* 3.7 24.1 - - + +
3E ILE* 3.1 35.2 - - + -
2F ARG* 1.3 73.7 - - - +
4F GLY* 1.3 65.4 + - - +
51F ALA* 3.3 9.0 + - - -
151F VAL* 4.7 0.2 - - + -
152F ALA 3.3 16.4 - - - +
153F LEU* 3.8 13.0 - - + -
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Residues in contact with GLY 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D ASP* 3.4 8.3 - - - -
151D VAL* 4.1 3.4 - - - -
3F ILE* 1.3 76.5 - - - +
5F HIS* 1.3 59.4 - - - +
47F ALA* 3.1 25.1 - - - -
51F ALA* 3.5 5.1 - - - +
151F VAL* 3.3 7.3 - - - +
152F ALA 2.9 32.9 + - - -
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Residues in contact with HIS 5 (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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5D HIS* 5.2 0.4 - + - -
95D ASP* 2.6 15.7 + - - +
97D THR* 3.0 21.7 + - - +
130D LYS* 2.7 31.9 + - - -
149D GLU* 2.8 37.8 + - + +
151D VAL* 3.5 30.7 - - + +
5E HIS* 5.0 4.5 - + - -
4F GLY* 1.3 74.8 - - - +
6F GLY* 1.3 66.8 + - - +
7F PHE* 3.8 12.6 - - + -
47F ALA* 3.5 6.8 - - - +
149F GLU* 2.6 30.0 + - - -
150F ALA 3.4 15.9 - - - -
151F VAL* 4.2 12.1 - - + -
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Residues in contact with GLY 6 (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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97D THR* 4.9 0.4 - - - -
130D LYS* 5.3 0.2 - - - -
5F HIS* 1.3 81.3 + - - +
7F PHE* 1.3 62.1 + - - +
43F ALA* 3.2 28.0 - - - -
46F ASP* 3.8 6.3 - - - -
47F ALA* 3.4 6.0 - - - +
149F GLU* 3.6 2.8 - - - -
150F ALA 2.7 35.4 + - - +
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Residues in contact with PHE 7 (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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97D THR* 4.1 13.8 - - + +
99D ILE* 3.9 27.6 - - + -
130D LYS* 5.7 0.4 - - - +
132D THR* 3.7 26.4 + - + +
133D THR 5.5 0.2 - - - -
134D THR* 4.1 14.4 - - + -
8903D GPP 3.6 33.7 - - + -
5F HIS* 3.8 14.3 + + + -
6F GLY* 1.3 74.3 - - - +
8F ASP* 1.3 62.0 + - - +
9F VAL* 3.6 30.7 - - + -
43F ALA* 4.1 3.2 - - - +
46F ASP* 4.2 8.1 - - - +
99F ILE* 4.7 3.4 - - + -
139F PHE* 5.4 0.4 - + - -
147F ALA* 4.3 17.5 - - + -
148F CYS 3.4 9.6 - - - -
149F GLU* 3.4 29.2 - - + -
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Residues in contact with ASP 8 (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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132D THR* 4.2 7.4 - - - +
6901D 1AA 3.0 12.0 + - - +
7F PHE* 1.3 77.4 - - - +
9F VAL* 1.3 77.6 + - - +
10F HIS* 3.1 11.0 + - - -
39F VAL* 3.6 23.1 - - + +
42F HIS* 3.0 14.4 - - + +
43F ALA* 3.9 8.5 - - - +
46F ASP* 5.5 2.5 - - - +
147F ALA* 3.4 1.2 - - - +
148F CYS 2.9 33.1 + - - +
6900F ZN 2.2 36.3 - - - -
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Residues in contact with VAL 9 (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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133D THR 4.5 5.4 + - - +
134D THR* 3.3 43.7 - - + +
135D GLU* 3.5 14.2 + - - +
137D LEU* 3.8 9.9 - - + -
6901D 1AA 4.7 1.2 + - - +
7F PHE* 3.6 28.7 - - + -
8F ASP* 1.3 88.4 + - - +
10F HIS* 1.3 75.7 + - - +
39F VAL* 3.8 0.2 - - - -
139F PHE* 3.6 30.3 - - + -
146F ILE 3.5 5.6 - - - +
147F ALA* 3.9 5.2 - - + -
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Residues in contact with HIS 10 (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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135D GLU* 2.6 30.2 + - - -
137D LEU* 4.3 0.3 - - - +
6901D 1AA 3.3 10.8 - - - -
8F ASP* 3.3 9.4 - - - -
9F VAL* 1.3 75.5 + - - +
11F ALA* 1.3 61.5 + - - +
31F LEU* 3.5 18.5 - - + +
32F LEU 3.4 11.8 + - - +
33F ALA* 3.6 18.2 - - + -
37F GLY* 3.7 21.9 - - - +
39F VAL* 3.3 19.0 - - + +
42F HIS* 3.2 8.5 + - - -
145F GLY* 3.3 1.6 - - - -
146F ILE 2.9 32.0 + - - -
6900F ZN 2.3 35.0 - - - -
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Residues in contact with ALA 11 (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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135D GLU* 3.1 22.0 + - + +
137D LEU* 3.7 27.6 - - + +
10F HIS* 1.3 73.6 - - - +
12F PHE* 1.3 65.5 + - - +
31F LEU* 3.3 7.2 - - - +
32F LEU* 3.1 34.9 + - + +
144F GLU 3.6 8.3 - - - +
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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