Contacts of the strand formed by residues 145 - 155 (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 GLY 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A HIS 3.3 13.5 - - - -
12A PHE* 3.5 14.2 - - - -
99A ILE 4.7 0.2 - - - +
100A ALA* 5.2 1.2 - - - -
139A PHE* 3.4 5.2 + - - -
140A THR* 3.4 26.1 - - - +
144A GLU* 1.3 82.9 - - - +
146A ILE* 1.3 66.7 + - - +
147A ALA 4.2 0.4 - - - -
137B LEU* 4.0 10.8 - - - +
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Residues in contact with ILE 146 (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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9A VAL* 3.6 1.1 - - - -
10A HIS 3.1 29.4 + - - +
12A PHE* 3.4 36.3 - - + -
18A ILE* 3.7 23.8 - - + -
20A ILE* 4.1 8.3 - - + -
31A LEU* 4.2 5.6 - - + +
39A VAL* 3.4 27.7 - - + +
98A ILE* 3.9 11.0 - - + -
99A ILE 3.5 9.2 - - - +
100A ALA* 3.8 17.0 - - + -
102A ALA 4.3 2.7 - - - +
105A MET* 4.1 12.3 - - + -
139A PHE* 4.6 2.7 - - - -
140A THR* 4.3 0.4 - - - -
145A GLY* 1.3 73.4 - - - +
147A ALA* 1.3 74.5 + - - +
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Residues in contact with ALA 147 (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* 4.1 11.4 - - + -
8A ASP 3.4 9.0 - - - +
9A VAL* 4.1 2.0 - - + -
39A VAL* 4.8 0.2 - - - -
99A ILE* 2.8 49.6 + - + +
139A PHE* 4.1 15.0 - - + -
140A THR* 3.5 19.1 - - + +
146A ILE* 1.3 81.5 - - - +
148A CYS* 1.3 62.2 + - - +
7903A GPP 4.6 3.1 - - + -
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Residues in contact with CYS 148 (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* 3.4 6.3 - - - -
8A ASP 2.9 31.4 + - - +
39A VAL* 3.4 28.3 - - + +
40A ALA* 3.4 27.6 - - - +
43A ALA* 3.3 9.7 - - - +
96A VAL* 3.5 15.7 - - - -
97A THR 3.5 10.3 - - - -
98A ILE* 4.2 6.1 - - + -
147A ALA* 1.3 77.0 - - - +
149A GLU* 1.3 76.3 + - - +
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Residues in contact with GLU 149 (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* 2.5 34.9 + - - -
6A GLY 3.5 1.7 - - - +
7A PHE* 3.9 7.6 - - + -
96A VAL* 3.6 0.2 - - - -
97A THR* 2.7 38.8 + - - +
99A ILE* 3.7 22.4 - - + -
148A CYS* 1.3 81.4 - - - +
150A ALA* 1.3 61.1 + - - +
7903A GPP 4.6 1.7 - - - +
149B GLU* 2.6 17.6 - - - +
5C HIS* 3.4 31.2 - - + +
7C PHE* 5.1 0.4 - - + -
149C GLU* 2.6 30.2 - - - +
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Residues in contact with ALA 150 (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* 3.4 5.6 - - - -
6A GLY 2.7 33.8 + - - +
43A ALA* 3.5 32.1 - - + +
44A LEU* 3.7 12.3 - - + +
47A ALA* 3.8 2.7 - - + -
95A ASP 3.3 10.5 - - - +
96A VAL* 4.2 10.1 - - + -
149A GLU* 1.3 79.1 + - - +
151A VAL* 1.3 65.0 + - - +
5C HIS* 5.4 1.3 - - - -
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Residues in contact with VAL 151 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A ILE* 4.6 10.5 - - + -
4A GLY 3.3 11.2 - - - +
5A HIS* 4.2 16.2 - - + -
44A LEU* 5.4 0.5 - - - +
47A ALA* 4.1 2.5 - - - -
94A VAL* 3.4 4.0 - - - +
95A ASP* 2.9 49.9 + - + +
150A ALA* 1.3 80.3 - - - +
152A ALA* 1.3 61.6 + - - +
151B VAL* 4.7 5.4 - - + -
3C ILE* 3.8 26.2 - - + +
4C GLY 4.0 0.2 - - - -
5C HIS* 3.5 37.5 - - + +
151C VAL* 4.8 4.0 - - + -
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Residues in contact with ALA 152 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2A ARG 3.5 0.6 - - - +
3A ILE* 3.3 9.9 - - - +
4A GLY 3.0 28.6 + - - +
44A LEU* 5.7 0.2 - - + -
47A ALA* 4.0 21.8 - - + +
48A LEU* 3.9 21.3 - - + +
51A ALA* 4.4 3.3 - - + +
93A ASN 3.7 4.5 - - - -
94A VAL* 3.8 17.3 - - + -
151A VAL* 1.3 76.3 - - - +
153A LEU* 1.3 61.7 + - - +
154A LEU* 4.0 0.7 - - + -
3C ILE* 3.9 3.8 - - - -
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Residues in contact with LEU 153 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 3.7 22.4 - - + -
2A ARG 3.3 14.4 - - - +
3A ILE* 4.0 10.1 - - + -
91A LEU* 4.3 1.2 - - - +
92A GLY* 2.8 31.5 + - - -
93A ASN* 2.9 23.7 + - - +
152A ALA* 1.3 74.6 - - - +
154A LEU* 1.3 57.8 + - - +
153B LEU* 3.9 28.7 - - + -
1C MET* 3.4 30.5 - - + +
2C ARG* 3.9 1.6 - - - -
3C ILE* 3.6 28.0 - - + +
153C LEU* 3.9 10.5 - - + -
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Residues in contact with LEU 154 (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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1A MET* 3.2 9.7 - - - +
2A ARG* 2.8 35.7 + - + +
48A LEU* 3.6 26.9 - - + +
51A ALA* 3.6 26.2 - - + -
52A ALA 4.0 7.4 - - - +
81A TRP* 3.7 27.6 - - + -
84A ILE* 3.7 19.3 - - + -
89A TYR* 3.9 20.2 - - + -
90A THR 3.4 14.4 - - - +
91A LEU* 4.0 7.6 - - + -
152A ALA* 5.2 0.7 - - + -
153A LEU* 1.3 74.2 - - - +
155A ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 155 (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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1A MET* 3.8 29.6 - - + +
2A ARG* 6.6 0.2 - - - -
88A GLY 4.0 1.0 - - - +
89A TYR* 3.4 10.0 - - - -
90A THR* 2.8 47.8 + - - +
91A LEU 3.8 8.5 - - - +
92A GLY* 3.8 22.4 - - - -
154A LEU* 1.3 79.7 - - - +
156A LYS* 1.3 72.7 - - - +
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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