Contacts of the strand formed by residues 82 - 90 (chain I) in PDB entry 2IAN
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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35I HIS* 4.1 4.0 - - - -
37I ASN* 4.6 9.2 - - - -
38I PRO* 4.8 8.1 - - - -
80I ASP 3.6 2.0 + - - -
81I SER* 1.3 75.4 - - - +
83I VAL* 1.3 62.6 + - - +
84I TYR* 4.5 3.6 - - - -
102I THR 3.8 0.2 - - - +
103I ARG* 3.5 4.4 - - - +
104I LEU* 2.7 43.0 + - - +
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Residues in contact with VAL 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34I PHE 3.8 0.3 - - - +
35I HIS* 2.3 36.9 + - - +
36I GLN* 3.9 15.6 - - + +
37I ASN 4.9 0.8 - - - +
82I GLY* 1.3 79.7 - - - +
84I TYR* 1.3 62.9 + - - +
85I PHE* 3.5 38.5 + - + -
100I GLN 5.0 1.8 - - - +
101I GLY* 4.2 10.8 - - - -
102I THR 3.5 7.6 - - - +
103I ARG* 4.1 25.1 - - + +
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Residues in contact with TYR 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I GLN* 2.7 22.2 - - - +
20I LEU* 3.4 23.8 - - + -
33I TRP* 4.5 2.0 - - + -
34I PHE 3.3 7.0 - - - +
35I HIS* 3.3 23.1 + + - -
45I LEU* 3.7 21.8 - - + -
58I LEU* 5.3 4.5 - - + +
71I LEU* 3.5 24.0 - - + -
73I ILE* 3.8 17.9 - - + +
80I ASP* 2.4 44.9 + - - +
82I GLY 4.5 2.0 - - - -
83I VAL* 1.3 75.0 - - - +
85I PHE* 1.3 57.2 + - - +
101I GLY* 2.9 3.0 - - - -
102I THR 2.8 28.2 + - - +
104I LEU* 3.6 31.9 - - + -
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Residues in contact with PHE 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I GLN* 3.4 2.0 - - - +
33I TRP* 3.4 6.4 - - - -
34I PHE* 2.6 42.9 + - + +
36I GLN* 3.6 21.1 - - + -
42I LEU* 4.0 20.9 - - + -
83I VAL* 3.5 28.5 - - + -
84I TYR* 1.3 73.4 - - - +
86I CYS* 1.3 56.8 + - - +
98I PHE* 3.6 27.6 - + + -
99I GLY 3.4 25.6 - - - -
100I GLN 4.1 13.7 - - - -
101I GLY* 3.9 6.5 - - - -
37J GLN* 3.8 20.9 - - - -
41J MET 4.6 4.3 - - - -
42J GLY* 4.7 2.2 - - - -
43J LEU* 4.6 17.7 - - + -
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Residues in contact with CYS 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I VAL* 3.1 19.7 - - - -
5I GLN* 3.2 17.6 + - - +
22I CYS* 2.1 53.2 - - + -
31I LEU* 4.2 3.8 - - + -
32I GLN 3.2 13.2 - - - +
33I TRP* 3.9 14.8 - - + -
85I PHE* 1.3 74.6 - - - +
87I ALA* 1.3 63.7 + - - +
98I PHE* 3.8 2.9 - - - -
99I GLY 3.1 24.4 + - - -
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Residues in contact with ALA 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I VAL* 4.9 1.1 - - - -
31I LEU* 3.4 6.3 - - - +
32I GLN* 2.7 33.5 + - + +
34I PHE* 4.2 11.2 - - + -
86I CYS* 1.3 78.6 - - - +
88I ALA* 1.3 61.7 - - - +
96I LEU* 4.1 14.1 - - + -
97I VAL 3.2 13.7 - - - +
98I PHE* 3.8 29.2 - - + -
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Residues in contact with ALA 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3I VAL* 4.4 8.7 - - + +
28I VAL* 3.6 28.7 - - + -
29I ASN* 3.5 14.6 - - - +
30I ASN 4.6 1.6 - - - -
31I LEU* 4.3 16.2 - - + +
87I ALA* 1.3 76.7 - - - +
89I LEU* 1.3 61.6 + - - +
90I ILE 4.0 0.2 - - - -
95I LYS 3.7 0.9 - - - +
96I LEU* 3.5 8.4 - - - +
97I VAL* 3.1 33.4 + - + +
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Residues in contact with LEU 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28I VAL* 4.0 0.9 - - - -
29I ASN* 2.7 42.3 + - - +
30I ASN* 4.3 28.5 - - + +
32I GLN* 4.5 9.4 - - - +
47I TYR* 5.9 0.2 - - + -
88I ALA* 1.3 70.6 - - - +
90I ILE* 1.3 65.9 + - - +
91I GLN* 3.3 1.9 + - - +
94I GLN* 3.4 39.9 - - + +
95I LYS 3.4 7.2 - - - +
96I LEU* 4.1 19.5 - - + +
31J TYR* 4.9 3.6 - - + -
33J TYR* 5.0 2.5 - - - +
94J THR* 4.9 9.9 - - + +
95J TYR 4.8 13.2 - - - +
96J HIS 6.2 1.3 - - - +
97J GLY* 4.8 5.8 - - - +
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Residues in contact with ILE 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F GLU* 5.6 2.2 - - + -
25H LEU* 5.0 7.9 - - + -
1I ILE* 4.4 20.9 - - + +
27I SER* 3.4 12.8 - - - +
28I VAL* 3.8 13.8 - - + +
88I ALA 3.9 1.2 + - - -
89I LEU* 1.3 71.1 - - - +
91I GLN* 1.3 71.9 + - - +
92I GLY 3.3 1.0 + - - -
93I ALA* 2.3 42.3 - - + +
94I GLN* 3.6 4.7 + - - -
95I LYS* 2.8 42.1 + - + +
97I VAL* 4.2 16.4 - - + -
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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