Contacts of the strand formed by residues 41 - 46 (chain B) in PDB entry 2IGT
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 TYR 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLU 3.9 0.3 - - - +
37B GLN* 3.4 6.0 + - - -
38B TYR* 2.8 39.2 + - - +
39B GLY 3.2 0.2 - - - -
40B ASP* 1.3 93.1 - - + +
42B ARG* 1.3 58.7 + - - +
43B VAL* 4.0 13.6 + - + -
65B ASP* 3.5 17.3 - - + +
87B LEU* 3.8 33.6 - - + +
88B GLY 4.6 5.8 + - - -
90B THR 4.8 4.2 + - - -
91B TRP* 3.3 56.5 - + + +
104B PHE* 3.8 21.5 - + + -
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Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ILE* 3.3 20.9 - - + +
35B LEU* 3.9 15.2 - - + +
36B GLU 3.4 6.1 - - - +
37B GLN* 2.5 37.3 + - - +
41B TYR* 1.3 72.7 - - - +
43B VAL* 1.3 61.1 + - - +
60B VAL* 3.7 19.0 + - - +
63B ASN* 5.5 5.2 - - - +
64B ALA* 3.7 8.5 - - - +
65B ASP* 2.8 46.5 + - - +
66B ALA 3.3 5.7 + - - -
289B LEU* 3.4 37.0 + - - +
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B LYS 3.7 0.9 - - - +
35B LEU* 3.4 5.5 - - - +
36B GLU* 2.8 45.8 + - - +
38B TYR* 3.6 36.1 - - + -
41B TYR* 4.4 17.7 - - + +
42B ARG* 1.3 79.2 - - - +
44B VAL* 1.3 63.1 + - - +
45B ARG* 4.4 8.7 - - + +
66B ALA* 3.1 22.7 - - + +
80B TRP* 4.4 9.4 - - + -
91B TRP* 4.9 5.2 - - + -
104B PHE* 4.4 11.7 - - + -
110B VAL* 5.1 2.5 - - + -
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Residues in contact with VAL 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.3 18.4 - - + -
34B LYS 3.3 7.6 - - - +
35B LEU* 3.7 18.2 - - + -
43B VAL* 1.3 70.9 - - - +
45B ARG* 1.3 69.9 + - - +
61B TRP* 3.8 32.1 - - + +
64B ALA* 3.7 23.8 - - + -
66B ALA 2.9 6.7 + - - +
67B ILE* 3.9 26.0 - - + -
68B PHE 2.9 28.0 + - - +
80B TRP* 4.1 0.3 - - - -
-3C TYR* 4.8 4.0 - - + +
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Residues in contact with ARG 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 3.4 7.8 - - - +
34B LYS* 2.9 54.5 + - - +
36B GLU* 2.8 40.1 + - - +
38B TYR* 3.2 13.3 + - - -
43B VAL* 4.2 5.5 - - + +
44B VAL* 1.3 81.4 - - - +
46B PRO* 1.3 73.7 - - + +
68B PHE* 4.5 2.2 - - + -
80B TRP* 3.8 22.0 - - + -
108B ARG* 2.9 49.3 + - - +
109B HIS* 4.0 0.4 - - - +
110B VAL* 3.9 12.1 - - - +
112B VAL 5.4 0.2 + - - -
114B PRO* 5.8 0.8 - - - +
1014B FMT 3.0 24.2 + - - -
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Residues in contact with PRO 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B GLY 3.5 9.6 - - - +
33B LEU* 3.8 8.7 - - + -
34B LYS* 4.0 1.2 - - - -
45B ARG* 1.3 89.7 - - + +
47B GLU* 1.3 59.6 + - - +
48B ALA 4.2 1.6 - - - +
68B PHE* 3.7 41.3 - - + +
70B GLY 6.0 1.6 - - - +
108B ARG* 2.8 42.2 + - + +
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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