Contacts of the strand formed by residues 127 - 132 (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 VAL 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A VAL* 3.9 11.9 - - + -
113A ARG* 2.8 57.0 + - + +
116A ILE* 3.9 31.9 - - + -
117A ALA* 4.2 7.6 - - + -
120A LEU* 5.2 0.4 - - + -
122A CYS* 3.6 29.6 - - - -
123A HIS 3.8 4.3 - - - +
124A MET* 2.9 12.8 + - - +
125A ASP 3.3 0.2 - - - -
126A ASP* 1.3 80.8 - - - +
128A ASN* 1.3 62.1 + - - +
129A VAL* 4.2 9.4 - - + -
53C ALA* 4.2 4.0 - - - +
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Residues in contact with ASN 128 (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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94A VAL 3.0 10.7 + - - +
95A ASP* 2.8 26.9 + - - +
96A VAL* 2.8 24.9 + - - +
113A ARG* 4.5 4.4 + - - +
126A ASP 4.2 0.2 - - - -
127A VAL* 1.3 76.1 - - - +
129A VAL* 1.3 71.6 + - - +
130A LYS* 3.7 7.9 - - - +
2C ARG* 5.8 0.2 - - - +
50C GLY* 3.2 28.5 - - - +
53C ALA* 3.4 13.7 - - + +
55C GLY* 3.0 45.9 + - - -
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Residues in contact with VAL 129 (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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40A ALA* 6.0 0.9 - - + -
96A VAL* 3.4 20.0 - - + +
98A ILE* 3.7 28.7 - - + -
109A ILE* 3.4 37.1 - - + +
112A MET* 3.9 11.7 - - + -
113A ARG* 4.1 17.0 - - + +
116A ILE* 3.8 28.7 - - + -
127A VAL* 4.2 3.1 - - + -
128A ASN* 1.3 86.0 + - - +
130A LYS* 1.3 65.1 + - - +
55C GLY* 4.8 5.4 - - - -
56C ASP* 5.0 0.2 - - - +
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Residues in contact with LYS 130 (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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95A ASP* 2.8 26.1 + - - -
96A VAL 2.7 12.4 + - - +
97A THR* 2.7 26.6 + - + +
98A ILE* 2.7 36.0 + - - +
109A ILE* 3.9 8.3 - - - -
128A ASN* 3.7 4.5 - - - +
129A VAL* 1.3 75.6 - - - +
131A ALA* 1.3 57.1 + - - +
5C HIS 2.6 30.1 + - - -
6C GLY* 4.5 1.1 - - - -
46C ASP* 3.3 29.8 - - + +
55C GLY 3.4 20.9 - - - +
56C ASP* 3.2 29.6 - - + +
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Residues in contact with ALA 131 (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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97A THR* 5.2 0.4 - - - -
98A ILE* 3.2 10.5 - - + +
105A MET* 3.8 21.5 - - + -
109A ILE* 4.2 3.0 - - + +
130A LYS* 1.3 80.8 - - - +
132A THR* 1.3 63.6 + - - +
46C ASP* 5.0 2.6 - - - +
56C ASP* 3.6 7.4 + - - +
3901C 1AA 3.3 60.2 + - + +
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Residues in contact with THR 132 (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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97A THR* 4.0 16.2 - - + -
98A ILE 2.9 9.4 + - - +
99A ILE* 3.5 5.7 - - + -
100A ALA 3.0 24.1 + - - -
131A ALA* 1.3 76.2 - - - +
133A THR* 1.3 72.0 + - - +
7C PHE* 3.5 42.1 + - + +
8C ASP* 3.6 16.1 + - - -
46C ASP* 5.0 5.4 - - - -
3901C 1AA 3.5 20.9 + - - -
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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