Contacts of the strand formed by residues 66 - 71 (chain D) in PDB entry 2IBS
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 ARG 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40D GLY 4.6 4.3 + - - +
41D GLY 2.9 13.2 + - - +
42D ARG* 3.6 34.4 - - + +
43D VAL* 2.8 34.3 + - - +
65D TYR* 1.3 71.3 - - - +
67D PHE* 1.3 60.8 + - - +
68D VAL* 4.0 13.9 + - + +
84D GLU* 2.9 37.1 + - - +
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Residues in contact with PHE 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D VAL* 3.6 18.2 - - + -
54D LEU* 3.9 26.5 - - + -
57D PHE* 3.6 24.9 - + + -
58D ARG* 3.6 36.8 - - + -
62D GLY 3.8 10.1 - - - -
63D THR 4.3 3.4 - - - -
65D TYR* 3.7 34.8 - + + -
66D ARG* 1.3 73.9 - - - +
68D VAL* 1.3 63.8 + - - +
82D TRP* 3.5 40.3 + + + +
83D ALA* 3.4 8.2 - - + -
84D GLU* 2.9 24.7 + - - +
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Residues in contact with VAL 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ARG* 5.6 1.3 - - - +
43D VAL 2.8 13.1 + - - +
44D LEU* 3.3 16.9 - - + -
45D GLU 2.9 24.5 + - - -
54D LEU* 3.5 11.1 - - - +
66D ARG* 4.0 19.7 - - + +
67D PHE* 1.3 80.9 - - - +
69D GLY* 1.3 62.3 + - - +
70D VAL* 4.7 0.2 - - + -
84D GLU* 3.5 24.7 - - + +
86D ILE* 3.8 29.2 - - + -
99D PHE* 3.9 28.3 - - + -
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Residues in contact with GLY 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 4.5 0.2 - - - -
45D GLU 3.4 9.2 - - - -
48D CYS* 3.6 18.3 - - - -
54D LEU* 4.2 2.9 - - - -
68D VAL* 1.3 74.3 - - - +
70D VAL* 1.3 65.3 + - - +
77D LEU* 4.6 0.2 - - - +
79D LEU* 3.9 9.1 - - - +
84D GLU 2.9 12.4 + - - +
85D GLY* 3.6 1.7 - - - -
86D ILE* 2.9 26.7 + - - +
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Residues in contact with VAL 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D LEU* 3.8 20.6 - - + -
45D GLU 3.1 8.7 + - - +
46D PRO* 4.7 0.4 - - + -
47D ALA* 2.8 29.8 + - - -
48D CYS* 3.3 5.2 + - - -
69D GLY* 1.3 76.4 - - - +
71D GLU* 1.3 63.9 + - - +
86D ILE* 3.5 15.3 - - + +
88D ALA* 3.6 27.6 - - + +
90D PHE* 4.1 29.6 - - + -
93D TRP* 3.8 31.4 - - + -
1002D NEA 4.0 0.6 - - - -
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Residues in contact with GLU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ALA 4.0 0.2 - - - -
48D CYS* 3.9 8.5 + - - -
49D ALA* 3.2 18.6 + - - +
69D GLY 4.2 0.2 - - - -
70D VAL* 1.3 76.1 - - - +
72D ILE* 1.3 62.4 + - - +
73D ASP* 2.8 35.9 + - - +
76D ALA* 3.7 8.7 - - - -
77D LEU* 3.7 34.3 - - + +
86D ILE 2.9 5.9 + - - -
87D LEU* 3.1 13.7 - - - +
88D ALA 3.0 21.5 + - - -
1002D NEA 2.6 48.6 + - - -
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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