Contacts of the strand formed by residues 2 - 12 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1D MET* 1.3 90.4 - - + +
3D ILE* 1.3 60.2 + - - +
50D GLY 4.9 0.2 + - - -
51D ALA* 2.9 33.4 + - - +
53D ALA* 3.6 14.8 - - - +
89D TYR* 3.7 33.9 + - + -
152D ALA 3.5 0.9 - - - +
153D LEU* 3.2 7.6 - - - -
154D LEU* 2.8 44.0 + - + +
156D LYS 5.4 2.7 - - - -
92E GLY 4.6 2.2 + - - -
93E ASN* 3.5 29.9 - - - +
125E ASP* 2.7 29.3 + - - -
126E ASP* 2.9 29.1 + - - +
153E LEU* 3.9 2.2 - - - -
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Residues in contact with ILE 3 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D ARG* 1.3 73.9 - - - +
4D GLY* 1.3 64.4 + - - +
51D ALA* 3.2 8.8 + - - -
151D VAL* 4.6 2.2 - - + -
152D ALA 3.4 14.8 - - - +
153D LEU* 3.9 9.4 - - + -
3E ILE* 4.0 9.6 - - + -
93E ASN* 2.8 49.1 + - - +
94E VAL* 5.2 0.2 - - - -
95E ASP* 4.1 4.0 - - - +
151E VAL* 3.7 31.6 - - + +
152E ALA* 4.0 3.1 - - - -
153E LEU* 3.6 35.0 - - + +
3F ILE* 3.6 36.1 - - + -
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Residues in contact with GLY 4 (chain D).
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* 1.3 76.3 - - - +
5D HIS* 1.3 60.7 + - - +
47D ALA* 3.1 24.2 - - - -
51D ALA* 3.5 4.4 - - - +
151D VAL* 3.2 9.4 - - - +
152D ALA 2.9 31.3 + - - -
95E ASP* 3.4 9.0 - - - -
151E VAL* 3.9 4.3 - - - -
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Residues in contact with HIS 5 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4D GLY* 1.3 75.0 - - - +
6D GLY* 1.3 68.0 + - - +
7D PHE* 3.8 14.6 - - + -
47D ALA* 3.5 5.7 - - - +
149D GLU* 3.1 31.6 + - + +
150D ALA 3.4 13.7 - - - -
151D VAL* 4.1 12.8 - - + -
5E HIS* 5.1 2.5 - + - -
95E ASP* 2.6 16.2 + - + +
97E THR* 3.1 22.1 + - - +
130E LYS* 2.6 32.2 + - - -
149E GLU* 3.4 34.4 + - + +
150E ALA* 5.7 0.2 - - - -
151E VAL* 3.6 29.2 - - + +
5F HIS* 5.2 0.2 - + - -
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Residues in contact with GLY 6 (chain D).
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* 1.3 81.2 - - - +
7D PHE* 1.3 61.2 + - - +
43D ALA* 3.1 26.9 - - - -
46D ASP* 3.8 5.8 - - - -
47D ALA* 3.4 5.8 - - - +
149D GLU* 3.4 3.8 - - - -
150D ALA 2.7 36.8 + - - +
97E THR* 4.8 0.4 - - - -
130E LYS* 4.9 0.4 - - - -
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Residues in contact with PHE 7 (chain D).
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* 3.8 14.3 + - + -
6D GLY* 1.3 74.6 - - - +
8D ASP* 1.3 61.6 + - - +
9D VAL* 3.6 31.4 - - + -
43D ALA* 4.1 3.2 - - - +
46D ASP* 4.1 11.0 - - - +
99D ILE* 5.1 0.4 - - + -
139D PHE* 5.2 1.1 - + - -
147D ALA* 4.2 12.3 - - + -
148D CYS 3.3 16.6 - - - -
149D GLU* 3.6 16.2 - - - -
8903D GPP 3.8 41.3 - - + -
97E THR* 4.1 14.8 - - + +
99E ILE* 3.8 32.5 - - + -
132E THR* 3.6 34.7 + - + +
134E THR* 4.2 3.8 - - + -
149E GLU* 4.1 3.4 - - - -
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Residues in contact with ASP 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 1.3 77.8 - - - +
9D VAL* 1.3 69.8 + - - +
10D HIS* 3.3 6.7 + - - -
39D VAL* 3.6 23.4 - - + +
42D HIS* 3.1 13.6 + - + +
43D ALA* 3.8 9.4 - - - +
46D ASP* 5.7 1.6 - - - +
147D ALA* 3.4 2.9 - - - +
148D CYS 2.8 38.0 + - - -
4900D ZN 2.0 30.3 - - - -
132E THR* 3.8 8.2 + - - -
4901E 1AA 3.0 26.4 + - - -
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Residues in contact with VAL 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 3.6 29.4 - - + -
8D ASP* 1.3 87.0 + - - +
10D HIS* 1.3 71.7 + - - +
39D VAL* 3.6 0.4 - - - -
139D PHE* 3.6 34.5 - - + -
146D ILE 3.4 7.9 - - - +
147D ALA* 3.8 6.1 - - + -
133E THR 4.2 4.8 + - - +
134E THR* 3.5 38.8 - - + +
135E GLU* 3.2 17.7 - - - +
137E LEU* 4.0 9.2 - - + -
4901E 1AA 3.9 0.9 + - - -
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Residues in contact with HIS 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D ASP* 3.4 1.1 - - - -
9D VAL* 1.3 77.6 + - - +
11D ALA* 1.3 61.5 + - - +
31D LEU* 3.4 17.8 - - + +
32D LEU 3.7 8.2 + - - +
33D ALA* 3.6 26.5 - - + +
37D GLY* 3.7 22.6 - - - +
39D VAL* 3.3 25.0 - - + +
42D HIS* 3.3 6.4 + - - -
145D GLY* 3.3 1.9 - - - -
146D ILE 3.0 32.1 + - - -
4900D ZN 2.1 37.1 - - - -
135E GLU* 3.7 9.1 + - - -
4901E 1AA 3.5 26.2 - - - -
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Residues in contact with ALA 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D HIS* 1.3 75.6 - - - +
12D PHE* 1.3 61.0 + - - +
31D LEU* 3.6 3.2 - - - -
32D LEU* 2.7 44.4 + - + +
144D GLU 3.5 8.3 - - - +
135E GLU* 4.2 18.9 - - + +
137E LEU* 3.7 26.4 - - + +
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Residues in contact with PHE 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C LYS* 6.1 0.2 - - - +
11D ALA* 1.3 79.6 - - - +
13D GLY* 1.3 58.5 + - - +
18D ILE* 4.3 5.8 - - + -
27D TYR* 3.5 39.0 - + - -
29D LYS* 3.8 23.6 - - + +
30D GLY 3.3 14.8 - - - +
31D LEU* 3.7 20.0 - - + -
32D LEU* 4.3 5.4 - - - +
102D ALA* 3.7 10.1 - - + -
143D GLY* 3.2 28.5 - - - +
144D GLU* 2.9 12.6 + - - +
145D GLY* 3.4 28.9 - - - -
146D ILE* 3.4 28.3 - - + -
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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