Contacts of the strand formed by residues 90 - 99 (chain C) 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 THR 90 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81C TRP* 3.7 10.8 - - - -
85C GLN* 4.7 10.3 - - - +
88C GLY 4.0 4.2 + - - +
89C TYR* 1.3 78.6 - - - +
91C LEU* 1.3 61.4 + - - +
154C LEU* 3.4 9.5 - - - +
155C ILE* 2.9 48.4 + - - +
156C LYS 5.1 1.6 + - - -
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Residues in contact with LEU 91 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C LEU* 3.7 30.1 - - + -
81C TRP* 3.5 23.1 - - + -
90C THR* 1.3 75.7 + - - +
92C GLY* 1.3 69.8 + - - +
93C ASN* 4.1 2.0 - - - +
94C VAL* 3.9 10.1 - - + -
120C LEU* 3.8 17.7 - - + -
122C CYS* 3.4 42.2 - - + -
126C ASP* 4.1 25.5 - - + +
127C VAL* 5.1 0.4 - - + -
153C LEU 4.7 1.3 - - - +
154C LEU* 4.2 4.3 - - + -
155C ILE* 3.7 11.2 - - - +
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Residues in contact with GLY 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET 5.4 5.6 - - - -
2B ARG* 5.1 1.2 + - - -
1C MET* 6.0 1.1 - - - -
90C THR 3.7 2.4 + - - -
91C LEU* 1.3 76.3 - - - +
93C ASN* 1.3 62.7 + - - +
126C ASP* 3.5 21.0 - - - +
153C LEU* 2.9 23.2 + - - -
155C ILE* 3.8 20.4 - - - +
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Residues in contact with ASN 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B MET 4.2 0.2 - - - +
2B ARG* 3.4 45.8 - - + +
3B ILE* 2.9 49.6 + - - +
50B GLY 4.4 2.2 + - - -
51B ALA 4.1 2.4 + - - -
91C LEU* 4.1 4.2 - - - +
92C GLY* 1.3 77.4 - - - +
94C VAL* 1.3 72.9 + - - +
126C ASP 3.3 13.5 - - - +
152C ALA* 3.7 0.7 - - - -
153C LEU* 3.0 33.8 + - - +
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Residues in contact with VAL 94 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ARG* 5.1 0.3 + - - -
3B ILE 5.0 0.2 - - - -
44C LEU* 3.6 32.5 - - + -
48C LEU* 4.1 10.8 - - + -
91C LEU* 3.9 21.5 - - + -
93C ASN* 1.3 86.4 + - - +
95C ASP* 1.3 64.0 + - - +
96C VAL* 4.9 3.8 - - + -
116C ILE* 4.4 6.1 - - + -
120C LEU* 4.3 4.3 - - + -
126C ASP 2.9 17.3 + - - +
127C VAL* 3.8 28.3 - - + -
128C ASN* 3.0 24.1 + - - +
151C VAL 3.5 4.3 - - - +
152C ALA* 4.1 6.3 - - + -
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Residues in contact with ASP 95 (chain C).
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 3.9 10.5 - - - +
4B GLY* 3.3 1.2 - - - -
5B HIS* 2.8 24.1 + - - +
50B GLY* 3.2 24.4 - - - +
94C VAL* 1.3 75.0 - - - +
96C VAL* 1.3 66.1 + - - +
97C THR* 5.1 0.2 - - - -
128C ASN* 2.9 21.8 + - - +
130C LYS* 2.8 30.2 + - - -
150C ALA* 3.4 2.6 - - - -
151C VAL* 2.9 49.9 + - + +
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Residues in contact with VAL 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40C ALA* 4.3 18.6 - - + +
44C LEU* 4.1 32.8 - - + -
94C VAL* 4.9 3.6 - - + -
95C ASP* 1.3 80.4 + - - +
97C THR* 1.3 61.8 + - - +
98C ILE* 4.0 2.0 - - + -
116C ILE* 4.8 4.3 - - + -
128C ASN 2.8 16.9 + - - +
129C VAL* 4.1 20.9 - - + -
130C LYS* 2.8 36.6 + - - +
148C CYS* 3.4 24.9 - - - -
149C GLU 3.6 3.1 - - - +
150C ALA* 4.4 4.7 - - + -
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Residues in contact with THR 97 (chain C).
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* 3.2 23.9 + - - +
7B PHE* 4.1 23.3 - - + +
96C VAL* 1.3 69.6 - - - +
98C ILE* 1.3 60.6 + - - +
99C ILE* 3.4 5.2 + - + +
130C LYS* 2.8 39.2 + - + -
132C THR* 4.1 24.2 - - + -
148C CYS* 3.3 4.8 - - - -
149C GLU* 2.6 43.0 + - - -
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Residues in contact with ILE 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ILE* 3.7 26.9 - - + -
39C VAL* 5.4 0.4 - - + -
40C ALA* 4.4 4.0 - - + -
96C VAL* 4.6 0.9 - - + -
97C THR* 1.3 72.3 - - - +
99C ILE* 1.3 60.8 + - - +
100C ALA* 3.7 4.1 + - + -
105C MET* 3.9 25.6 - - + -
109C ILE* 4.0 8.3 - - + -
112C MET* 3.7 11.9 - - + -
129C VAL* 3.7 26.9 - - + -
130C LYS 2.8 15.7 + - - +
131C ALA* 3.2 3.5 - - - +
132C THR* 2.8 29.5 + - - +
146C ILE* 3.9 23.6 - - + -
147C ALA 3.8 3.4 - - - +
148C CYS* 4.0 14.6 - - + -
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Residues in contact with ILE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7903A GPP 4.8 3.1 - - + -
7B PHE* 3.7 32.5 - - + -
7C PHE* 4.6 4.7 - - + -
97C THR* 3.8 9.6 - - + +
98C ILE* 1.3 72.4 - - - +
100C ALA* 1.3 62.5 + - - +
132C THR* 3.4 11.9 - - + +
134C THR* 3.6 31.0 - - + -
140C THR* 3.6 16.2 - - + +
146C ILE* 3.4 0.7 - - - +
147C ALA* 2.7 59.0 + - + +
149C GLU* 3.7 28.9 - - + +
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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