Contacts of the strand formed by residues 2 - 12 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B MET* 1.3 81.3 - - - +
3B ILE* 1.3 60.0 + - - +
50B GLY 4.8 1.4 + - - -
51B ALA* 2.7 31.0 + - - +
53B ALA* 3.5 17.0 - - - +
89B TYR* 3.4 30.0 + - + -
152B ALA 3.4 2.3 - - - +
153B LEU* 3.3 9.3 - - - -
154B LEU* 2.9 42.7 + - + +
156B LYS* 6.0 0.9 - - + -
92C GLY 5.1 0.9 + - - +
93C ASN* 3.4 34.0 - - + +
94C VAL 5.1 1.2 + - - -
125C ASP* 2.7 40.5 + - - -
126C ASP* 3.3 23.2 + - - +
153C LEU* 3.9 0.4 - - - -
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Residues in contact with ILE 3 (chain B).
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* 3.0 34.8 - - + -
2B ARG* 1.3 72.3 - - - +
4B GLY* 1.3 71.6 + - - +
51B ALA* 3.3 8.4 - - - -
151B VAL* 4.4 1.3 - - + -
152B ALA 3.4 11.9 - - - +
153B LEU* 3.9 7.6 - - + -
3C ILE* 3.6 15.5 - - + -
93C ASN* 2.9 42.7 + - - +
94C VAL* 5.1 0.7 - - - -
95C ASP* 3.9 5.7 - - - +
151C VAL* 3.6 25.4 - - + +
152C ALA* 3.8 6.7 - - - -
153C LEU* 3.7 33.9 - - + +
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Residues in contact with GLY 4 (chain B).
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* 1.3 77.7 - - - +
5B HIS* 1.3 60.0 + - - +
47B ALA* 3.2 24.5 - - - -
51B ALA* 3.6 2.9 - - - +
151B VAL* 3.2 10.0 - - - +
152B ALA 2.9 31.0 + - - -
95C ASP* 3.3 9.9 - - - -
151C VAL* 3.9 3.6 - - - -
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Residues in contact with HIS 5 (chain B).
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* 4.9 4.6 + + - -
4B GLY* 1.3 74.3 - - - +
6B GLY* 1.3 74.8 + - - +
7B PHE* 3.7 7.2 - - + -
47B ALA* 3.6 5.5 - - - -
149B GLU* 2.9 26.6 + - - +
150B ALA 3.3 13.5 - - - -
151B VAL* 4.3 12.3 - - + -
5C HIS* 4.9 4.0 - + - -
95C ASP* 2.8 9.0 + - - +
97C THR* 3.2 21.9 + - - +
130C LYS* 2.7 32.9 + - - -
149C GLU* 3.0 38.6 + - + +
150C ALA* 5.3 0.4 - - - -
151C VAL* 3.7 30.9 - - + +
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Residues in contact with GLY 6 (chain B).
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* 1.3 84.2 - - - +
7B PHE* 1.3 59.0 + - - -
43B ALA* 3.2 26.5 - - - -
46B ASP* 3.9 7.0 - - - -
47B ALA* 3.6 4.5 - - - +
149B GLU* 3.4 3.6 - - - -
150B ALA 2.7 36.4 + - - +
97C THR* 4.7 1.6 - - - -
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Residues in contact with PHE 7 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7903A GPP 3.7 39.5 - - + -
5B HIS* 3.7 14.5 + - + -
6B GLY* 1.3 74.3 - - - +
8B ASP* 1.3 63.0 + - - +
9B VAL* 3.6 30.1 - - + -
43B ALA* 4.1 2.6 - - - +
46B ASP* 4.4 8.4 - - - +
139B PHE* 5.2 2.9 - + - -
147B ALA* 4.1 12.6 - - + -
148B CYS 3.3 13.9 - - - -
149B GLU* 3.7 20.9 - - + -
97C THR* 4.1 14.3 - - + +
99C ILE* 3.7 30.1 - - + -
132C THR* 3.5 27.0 + - + +
134C THR* 4.0 15.7 - - + -
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Residues in contact with ASP 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PHE* 1.3 77.9 - - - +
9B VAL* 1.3 76.2 + - - +
10B HIS* 3.1 10.4 + - - -
39B VAL* 3.2 23.1 - - + +
42B HIS* 3.1 13.9 + - - +
43B ALA* 4.0 8.5 - - + +
46B ASP* 5.5 1.4 - - - +
57B ILE* 5.0 2.8 - - - +
147B ALA* 3.9 0.2 - - - +
148B CYS 2.9 32.9 + - - +
2900B ZN 2.1 36.8 - - - -
132C THR* 3.8 14.0 + - - -
133C THR 4.9 0.5 - - - +
2901C 1AA 3.5 7.3 + - - +
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Residues in contact with VAL 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PHE* 3.6 29.4 - - + -
8B ASP* 1.3 86.2 + - - +
10B HIS* 1.3 74.8 + - - +
39B VAL* 3.9 0.2 - - - -
139B PHE* 3.5 35.7 - - + -
146B ILE 3.4 7.0 - - - +
147B ALA* 3.8 5.2 - - + -
133C THR 4.5 5.1 + - - +
134C THR* 3.4 37.0 - - + +
135C GLU* 3.4 18.7 + - - +
137C LEU* 4.0 9.4 - - + -
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Residues in contact with HIS 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ASP* 3.2 9.6 - - - -
9B VAL* 1.3 78.1 + - - +
11B ALA* 1.3 60.4 + - - +
31B LEU* 3.3 20.7 - - + +
32B LEU 4.5 2.9 - - - +
33B ALA* 3.6 20.7 - - + +
35B SER* 4.0 0.7 - - - -
37B GLY* 3.5 25.6 - - - +
39B VAL* 3.9 11.8 - - + +
42B HIS* 3.1 6.6 + - - -
145B GLY* 3.3 2.1 - - - -
146B ILE 3.1 32.3 + - - +
2900B ZN 2.1 36.2 - - - -
135C GLU* 2.7 31.5 + - + +
2901C 1AA 3.8 13.7 - - - -
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Residues in contact with ALA 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B HIS* 1.3 75.1 - - - +
12B PHE* 1.3 66.1 + - - +
31B LEU* 3.6 3.3 - - - +
32B LEU* 2.9 30.6 + - + +
144B GLU 3.6 7.2 - - - +
135C GLU* 2.8 25.8 + - - +
137C LEU* 3.7 26.2 - - + -
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Residues in contact with PHE 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B HIS 4.0 0.4 + - - -
11B ALA* 1.3 79.6 - - - +
13B GLY* 1.3 57.7 + - - +
18B ILE* 4.3 3.8 - - + -
27B TYR* 3.6 38.8 - + - -
29B LYS* 4.0 20.9 - - + -
30B GLY 3.2 15.7 - - - +
31B LEU* 3.6 20.0 - - + -
32B LEU* 4.3 4.7 - - - +
102B ALA 3.8 10.1 - - - -
143B GLY* 3.0 33.2 - - - +
144B GLU* 3.0 23.0 + - - +
145B GLY* 3.5 17.0 - - - -
146B ILE* 3.6 28.0 - - + -
29E LYS* 5.5 1.7 - - - -
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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