Contacts of the strand formed by residues 82 - 90 (chain C) in PDB entry 2IAM
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 82 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35C HIS* 3.9 0.9 - - - -
36C GLN 3.5 10.5 - - - -
37C ASN 4.8 0.2 - - - -
38C PRO* 4.3 11.0 - - - +
80C ASP 3.5 0.8 + - - -
81C SER* 1.3 75.1 - - - +
83C VAL* 1.3 61.8 + - - -
84C TYR* 4.2 4.0 - - - -
103C ARG* 3.5 2.7 - - - +
104C LEU* 2.6 43.9 + - - +
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Residues in contact with VAL 83 (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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34C PHE 4.1 0.2 - - - +
35C HIS* 4.4 0.2 + - - -
36C GLN* 2.8 43.1 + - + +
82C GLY* 1.3 73.5 - - - -
84C TYR* 1.3 67.0 + - - +
85C PHE* 3.6 36.4 + - + -
100C GLN 4.8 2.0 - - - +
101C GLY* 4.1 2.7 - - - -
102C THR 3.1 18.2 - - - +
103C ARG* 3.6 31.0 - - + +
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Residues in contact with TYR 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5C GLN* 2.8 15.7 + - - +
20C LEU* 3.3 25.6 - - + -
33C TRP* 4.7 5.2 - - + -
34C PHE 3.3 5.8 - - - +
35C HIS* 3.3 31.1 + + + -
45C LEU* 3.9 17.7 - - + -
58C LEU* 5.3 3.8 - - + -
71C LEU* 3.7 23.6 - - + -
73C ILE* 4.3 9.3 - - + +
80C ASP* 2.5 45.3 + - - +
82C GLY 4.1 4.5 - - - -
83C VAL* 1.3 76.8 - - - +
85C PHE* 1.3 62.6 + - - +
101C GLY* 3.1 12.5 - - - -
102C THR 2.9 11.9 + - - +
104C LEU* 3.6 28.2 - - + +
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Residues in contact with PHE 85 (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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5C GLN* 3.1 4.9 - - - +
33C TRP* 3.4 5.5 - - - -
34C PHE* 2.8 44.5 + - + +
36C GLN* 3.5 31.6 - - + -
42C LEU* 4.3 17.5 - - + -
83C VAL* 3.6 24.0 - - + -
84C TYR* 1.3 75.0 - - - +
86C CYS* 1.3 61.0 + - - +
87C ALA 3.8 0.5 + - - -
98C PHE* 4.0 25.4 - + + -
99C GLY 3.6 20.9 - - - -
100C GLN 3.8 17.3 - - - -
101C GLY* 4.0 6.1 - - - -
37D GLN* 4.1 11.0 - - - -
41D MET 4.5 6.1 - - - -
42D GLY* 4.8 9.6 - - - -
43D LEU* 4.7 12.6 - - + -
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Residues in contact with CYS 86 (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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3C VAL* 3.2 15.6 - - - +
5C GLN* 2.7 21.4 - - - +
22C CYS* 2.1 53.6 - - + -
31C LEU* 4.4 7.0 - - + -
32C GLN 3.3 12.1 - - - +
33C TRP* 4.2 15.0 - - + -
85C PHE* 1.3 72.0 - - - +
87C ALA* 1.3 60.7 + - - +
98C PHE* 3.8 1.9 - - - -
99C GLY 3.2 21.3 + - - -
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Residues in contact with ALA 87 (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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3C VAL* 5.2 1.1 - - - -
31C LEU* 3.6 6.6 - - - +
32C GLN* 3.0 32.6 + - + +
34C PHE* 3.8 19.7 - - + -
85C PHE 3.8 1.2 + - - -
86C CYS* 1.3 76.8 - - - +
88C ALA* 1.3 64.5 + - - +
96C LEU* 4.5 9.0 - - + -
97C VAL 3.1 10.3 - - - +
98C PHE* 3.6 28.7 - - + -
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Residues in contact with ALA 88 (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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3C VAL* 4.2 11.0 - - + -
24C PHE* 5.3 1.6 - - + -
28C VAL* 3.8 25.8 - - + -
29C ASN* 3.4 16.4 - - - +
30C ASN 4.2 4.9 - - - -
31C LEU* 4.7 9.6 - - + -
32C GLN* 5.7 0.2 - - - -
87C ALA* 1.3 78.1 - - - +
89C LEU* 1.3 64.5 + - - +
95C LYS 3.3 0.9 - - - +
96C LEU* 3.5 2.5 - - - -
97C VAL* 2.7 40.1 + - - +
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Residues in contact with LEU 89 (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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70B GLN* 5.9 4.5 - - - +
28C VAL* 3.9 2.2 - - - -
29C ASN* 2.7 42.4 + - - +
30C ASN* 4.6 24.7 + - + +
32C GLN* 5.2 4.9 - - - +
88C ALA* 1.3 73.6 - - - +
90C ILE* 1.3 66.3 + - - +
91C GLN* 3.5 1.4 + - - -
94C GLN* 3.8 36.3 - - + +
95C LYS 3.3 5.8 - - - +
96C LEU* 3.4 32.8 - - + +
31D TYR* 5.0 8.1 - - + -
33D TYR* 4.8 6.1 - - - +
94D THR* 5.0 7.4 - - - +
95D TYR 5.3 4.9 - - - +
96D HIS 6.5 1.1 - - - -
97D GLY 5.7 1.6 - - - +
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Residues in contact with ILE 90 (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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55A GLU* 5.6 1.8 - - + +
1C ILE* 4.8 12.8 - - - +
27C SER* 3.4 14.4 - - - +
28C VAL* 3.6 17.7 - - + +
88C ALA 4.1 0.4 + - - -
89C LEU* 1.3 72.8 - - - +
91C GLN* 1.3 68.9 + - - +
92C GLY 3.2 0.7 + - - -
93C ALA* 2.3 44.2 - - + +
94C GLN* 3.5 5.2 + - - -
95C LYS* 3.1 49.4 + - + +
97C VAL* 4.2 13.5 - - + -
25P LEU* 4.7 12.3 - - + -
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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