Contacts of the strand formed by residues 2 - 11 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 80.8 - - - +
3A ILE* 1.3 61.0 + - - +
50A GLY 5.4 0.2 + - - -
51A ALA* 3.3 30.6 + - - +
53A ALA* 4.5 5.7 - - - +
89A TYR* 3.4 39.1 + - + -
152A ALA 3.5 0.5 - - - +
153A LEU* 3.3 5.2 - - - -
154A LEU* 2.8 43.2 + - + +
156A LYS* 5.6 3.1 - - + +
92B GLY 4.8 1.9 + - - +
93B ASN* 3.4 30.9 - - + +
125B ASP* 2.7 34.9 + - - +
126B ASP* 2.6 32.7 + - - +
153B LEU* 3.9 4.0 - - - -
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Residues in contact with ILE 3 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ARG* 1.3 75.2 - - - +
4A GLY* 1.3 74.7 + - - +
51A ALA* 3.4 7.8 - - - -
151A VAL* 4.6 4.0 - - + -
152A ALA 3.3 11.2 - - - +
153A LEU* 4.0 8.7 - - + -
3B ILE* 3.0 34.8 - - + -
93B ASN* 2.8 43.7 + - - +
95B ASP* 4.0 5.9 - - + +
151B VAL* 3.8 29.2 - - + -
152B ALA 4.3 0.7 - - - -
153B LEU* 3.7 27.3 - - + +
3C ILE* 3.7 23.1 - - + -
151C VAL* 5.7 0.2 - - + -
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Residues in contact with GLY 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ILE* 1.3 80.4 - - - +
5A HIS* 1.3 61.1 + - - +
47A ALA* 3.1 24.2 - - - -
51A ALA* 3.5 6.3 - - - +
151A VAL* 3.3 5.9 - - - +
152A ALA 3.0 28.2 + - - -
95B ASP* 3.3 10.3 - - - -
151B VAL* 4.2 3.1 - - - -
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Residues in contact with HIS 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A GLY* 1.3 73.6 - - - +
6A GLY* 1.3 66.9 + - - +
7A PHE* 3.8 10.8 - - + -
47A ALA* 3.5 5.7 - - - +
149A GLU* 2.5 34.3 + - - -
150A ALA 3.4 12.6 - - - -
151A VAL* 4.2 12.3 - - + -
5B HIS* 4.9 3.1 + + - -
95B ASP* 2.6 15.7 + - - +
97B THR* 3.3 18.9 + - - +
130B LYS* 2.8 31.9 + - - -
149B GLU* 3.6 35.6 + - + +
151B VAL* 3.8 29.2 - - + +
5C HIS* 4.9 7.3 + + - -
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Residues in contact with GLY 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A HIS* 1.3 75.2 - - - +
7A PHE* 1.3 62.1 + - - +
43A ALA* 3.1 28.9 - - - -
46A ASP* 3.8 5.8 - - - -
47A ALA* 3.3 7.3 - - - +
149A GLU* 3.5 8.3 - - - +
150A ALA 2.7 34.9 + - - +
130B LYS* 5.3 0.2 - - - -
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Residues in contact with PHE 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A HIS* 3.8 13.9 + - + -
6A GLY* 1.3 76.0 - - - +
8A ASP* 1.3 62.2 + - - +
9A VAL* 3.7 28.0 - - + -
43A ALA* 4.1 2.3 - - - +
46A ASP* 4.1 10.9 - - - +
99A ILE* 4.8 0.2 - - + -
139A PHE* 5.2 0.9 - + - -
147A ALA* 4.1 17.0 - - + -
148A CYS 3.4 11.4 - - - -
149A GLU* 3.9 13.7 - - + -
7903A GPP 3.8 36.8 - - + -
97B THR* 4.1 13.4 - - + +
99B ILE* 3.7 34.3 - - + -
130B LYS* 5.7 0.6 - - - +
132B THR* 3.6 30.6 + - + +
133B THR 5.2 0.2 - - - -
134B THR* 4.2 4.0 - - + -
149B GLU* 3.9 13.0 - - - +
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Residues in contact with ASP 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 1.3 76.4 - - - +
9A VAL* 1.3 73.5 + - - +
10A HIS* 3.3 6.1 + - - -
39A VAL* 3.5 25.4 - - - +
42A HIS* 3.0 16.1 + - + +
43A ALA* 3.9 9.4 - - - +
46A ASP* 5.2 2.9 - - - +
147A ALA* 3.4 4.2 - - - +
148A CYS 2.9 32.0 + - - -
1900A ZN 2.2 35.6 - - - -
1901A 1AA 3.0 13.1 + - - +
132B THR* 4.4 8.4 + - - -
133B THR 5.3 0.3 - - - +
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Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A PHE* 3.7 28.7 - - + -
8A ASP* 1.3 89.2 + - - +
10A HIS* 1.3 76.4 + - - +
39A VAL* 3.6 1.6 - - - -
139A PHE* 3.7 34.1 - - + -
146A ILE 3.6 5.6 - - - +
147A ALA* 4.1 2.7 - - + -
133B THR 4.1 5.9 + - - +
134B THR* 3.4 41.5 - - + +
135B GLU* 3.1 17.0 - - + +
137B LEU* 4.1 8.7 - - + -
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Residues in contact with HIS 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ASP* 3.3 9.4 - - - -
9A VAL* 1.3 77.0 + - - +
11A ALA* 1.3 64.0 + - - +
31A LEU* 3.5 22.5 - - + +
32A LEU 4.8 1.3 - - - +
33A ALA* 3.6 23.7 + - + +
34A HIS* 2.7 35.8 + + - -
37A GLY* 3.8 17.0 - - - +
39A VAL* 3.4 16.3 - - + +
42A HIS* 3.2 11.8 + - - -
145A GLY* 3.3 0.9 - - - -
146A ILE 3.1 31.1 + - - +
1900A ZN 2.1 30.5 - - - -
1901A 1AA 3.4 7.2 - - - -
135B GLU* 3.7 4.9 + - - -
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A HIS* 1.3 73.7 + - - +
12A PHE* 1.3 67.9 + - - +
31A LEU* 3.2 13.3 - - - +
32A LEU* 3.3 33.0 + - + +
144A GLU 3.5 7.6 - - - +
135B GLU* 4.3 17.5 + - + +
137B LEU* 3.8 25.6 - - + -
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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