Contacts of the strand formed by residues 28 - 36 (chain S) 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 VAL 28 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1S ILE 3.7 22.0 - - - +
2S GLN 4.4 3.6 - - - +
3S VAL* 4.7 2.7 - - + -
24S PHE* 3.3 47.0 - - + -
25S SER* 3.2 9.8 + - - +
26S ASP* 4.0 4.0 - - - +
27S SER* 1.3 89.5 - - - +
29S ASN* 1.3 69.7 + - - +
67S ARG* 5.1 0.2 - - - -
88S ALA* 3.7 17.0 - - + -
89S LEU 3.2 12.6 - - - +
90S ILE* 3.8 21.8 - - + +
91S GLN* 4.2 3.4 - - - +
97S VAL* 5.1 5.2 - - + -
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Residues in contact with ASN 29 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77Q THR* 3.4 30.0 - - - +
81Q HIS* 4.8 8.3 + - - +
24S PHE* 3.9 26.1 - - - -
26S ASP* 5.5 0.6 + - - -
28S VAL* 1.3 82.1 + - - +
30S ASN* 1.3 84.9 + - - +
31S LEU 3.4 2.4 + - - -
49S PRO 4.5 2.6 - - - +
64S ALA* 4.2 12.9 + - - +
67S ARG* 5.1 3.8 - - - +
88S ALA* 3.4 3.2 - - - +
89S LEU* 2.9 31.9 + - - +
91S GLN* 3.7 25.9 - - - +
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Residues in contact with ASN 30 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70Q GLN* 4.3 11.8 - - - +
77Q THR* 4.2 18.9 + - - +
29S ASN* 1.3 98.2 + - - +
31S LEU* 1.3 68.5 + - - +
32S GLN* 3.5 14.7 + - - +
47S TYR* 2.6 38.3 + - + -
49S PRO* 3.9 15.6 - - - +
87S ALA 4.4 1.2 - - - +
88S ALA* 4.4 2.1 - - - -
89S LEU* 4.7 21.6 + - + +
91S GLN* 5.4 3.8 + - - -
96T HIS 5.6 0.9 - - - -
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Residues in contact with LEU 31 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3S VAL* 5.1 0.9 - - + -
22S CYS* 3.6 26.9 - - - -
24S PHE* 3.1 42.4 - - + -
29S ASN* 3.4 0.6 + - - -
30S ASN* 1.3 81.1 - - - +
32S GLN* 1.3 60.6 + - - +
33S TRP* 5.8 0.9 - - - +
47S TYR* 3.9 0.7 - - - -
48S ILE* 3.0 40.3 + - + +
49S PRO* 4.7 1.0 + - - +
62S THR* 4.0 7.4 - - + +
69S SER* 3.0 35.2 - - - +
86S CYS* 3.7 8.1 - - + -
87S ALA 3.4 18.2 - - - +
88S ALA* 4.2 9.9 - - + -
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Residues in contact with GLN 32 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30S ASN* 3.5 10.4 + - - +
31S LEU* 1.3 79.8 - - - +
33S TRP* 1.3 65.6 + - - +
34S PHE* 3.3 25.6 - - + -
44S ASN* 3.4 5.0 + - - +
46S PHE 3.0 12.1 - - - +
47S TYR* 4.0 9.6 - - + +
48S ILE 4.7 0.2 - - - +
86S CYS* 3.0 11.1 - - - +
87S ALA 2.9 31.2 + - - +
88S ALA* 5.7 0.4 - - - +
89S LEU* 5.8 3.4 - - - +
96S LEU* 3.5 27.0 - - - +
94T THR* 4.6 2.2 - - - +
97T GLY 3.4 20.8 + - - -
98T THR* 3.6 1.2 - - - -
99T GLY* 2.7 29.2 + - - +
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Residues in contact with TRP 33 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5S GLN* 4.3 11.4 - - - -
20S LEU* 3.4 46.9 - - + -
21S ARG 4.0 2.9 - - - -
22S CYS* 3.7 21.1 - - + -
31S LEU* 5.8 0.6 - - + +
32S GLN* 1.3 74.4 - - - +
34S PHE* 1.3 59.2 + - - +
44S ASN* 4.0 1.2 + - - -
45S LEU* 2.8 51.4 + - + +
46S PHE* 2.9 14.8 + - + +
48S ILE* 4.2 9.6 - - + -
60S ALA* 4.1 19.5 - - + -
69S SER* 3.5 34.4 + - - -
70S LEU 3.9 7.7 + - - -
71S LEU* 3.6 26.9 - - + -
84S TYR* 4.6 5.8 - + + -
85S PHE 3.5 13.0 - - - -
86S CYS* 4.1 17.7 - - + +
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Residues in contact with PHE 34 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32S GLN* 3.3 33.4 - - + -
33S TRP* 1.3 76.5 - - - +
35S HIS* 1.3 59.8 + - - +
36S GLN 4.1 0.2 - - - -
42S LEU* 4.3 14.8 - - + -
43S ILE 3.4 17.0 - - - +
44S ASN* 3.4 18.4 - - + -
45S LEU* 4.0 3.8 - - - -
84S TYR* 3.1 8.1 - - - +
85S PHE* 2.7 48.1 + - + +
87S ALA* 3.6 28.3 - - + -
96S LEU* 5.1 2.7 - - + -
98S PHE* 3.9 15.7 - + + -
99T GLY* 3.5 23.1 - - - -
101T PHE* 3.9 30.7 - + - -
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Residues in contact with HIS 35 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34S PHE* 1.3 73.7 - - - +
36S GLN* 1.3 65.1 + - - +
37S ASN* 4.0 14.7 - - + +
42S LEU* 3.7 3.5 - - - +
43S ILE* 3.1 48.6 + - + +
45S LEU* 3.8 22.1 - - + +
79S THR 4.2 9.5 + - - -
80S ASP* 3.5 17.4 + - - -
81S SER 3.2 30.4 + - - -
82S GLY* 3.7 8.5 - - - -
83S VAL 3.4 3.4 + - - -
84S TYR* 3.3 27.6 + + + -
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Residues in contact with GLN 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34S PHE 4.1 0.2 - - - -
35S HIS* 1.3 68.1 - - - +
37S ASN* 1.3 71.4 + - - +
40S GLY* 2.6 38.5 + - - +
41S GLN 3.4 2.9 - - - +
42S LEU* 3.8 19.6 - - + +
82S GLY* 3.5 1.0 - - - -
83S VAL* 2.4 57.8 + - + +
85S PHE* 3.5 17.7 - - + -
37T GLN* 2.6 45.8 + - - -
43T LEU* 5.0 0.2 - - - +
90T PHE* 3.6 6.3 - - - -
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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