Contacts of the strand formed by residues 89 - 95 (chain D) in PDB entry 3UDB
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 HIS 89 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12D LEU* 5.2 4.9 - - + -
13D PRO* 3.0 39.6 - - + +
51D TYR* 4.6 10.3 + + + +
52D ILE 2.3 32.3 - - - +
53D GLU* 2.9 29.3 + - + +
54D ARG* 3.4 15.0 - - - +
85D LEU* 4.2 0.6 - - - -
86D THR* 2.8 34.0 + - - +
88D THR* 1.3 112.4 - - + +
90D LEU* 1.3 58.0 - - - +
91D ALA 4.0 0.2 + - - -
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Residues in contact with LEU 90 (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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50D LYS 3.6 1.0 - - - +
51D TYR* 3.4 6.5 - - - -
52D ILE* 2.7 42.7 + - + +
54D ARG* 4.5 2.2 - - - +
58D ILE* 5.3 9.0 - - + -
62D VAL* 4.8 9.6 - - + -
66D ILE* 3.8 29.4 - - + -
83D VAL* 4.0 12.8 - - + -
84D ILE 3.7 14.8 - - - +
85D LEU* 4.6 3.1 - - + +
89D HIS* 1.3 73.4 - - - +
91D ALA* 1.3 63.8 + - - +
92D ILE* 3.9 11.6 + - + +
311D ILE* 3.9 32.3 - - + +
312D ILE* 4.9 7.4 - - + -
315D ALA* 4.4 17.3 - - + -
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Residues in contact with ALA 91 (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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16D HIS* 4.2 8.3 - - - +
49D VAL* 4.0 10.3 - - + -
50D LYS 3.5 4.7 - - - -
51D TYR* 3.8 23.3 - - + -
82D GLU 4.0 0.2 - - - +
83D VAL* 3.4 7.4 - - - +
84D ILE* 2.7 52.0 + - + +
86D THR* 4.6 3.6 - - + -
89D HIS 4.0 0.6 + - - -
90D LEU* 1.3 74.0 - - - +
92D ILE* 1.3 61.9 + - - +
93D VAL* 3.9 2.4 + - + +
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Residues in contact with ILE 92 (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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48D ALA 3.7 1.2 - - - +
49D VAL* 3.4 1.7 - - - -
50D LYS* 2.7 47.1 + - + +
52D ILE* 3.7 32.5 - - + -
66D ILE* 4.0 22.0 - - + -
80D PHE* 4.1 20.6 - - + -
82D GLU 4.2 1.3 - - - -
83D VAL* 4.2 2.7 - - + -
90D LEU* 4.2 9.4 - - + +
91D ALA* 1.3 75.1 - - - +
93D VAL* 1.3 61.5 + - - +
94D MET* 3.8 11.3 - - + +
163D TYR* 3.5 48.0 - - + +
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Residues in contact with VAL 93 (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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16D HIS* 6.2 0.4 - - - +
21D TYR* 3.9 18.4 - - + +
47D VAL* 3.4 30.5 - - + -
48D ALA 3.5 3.1 - - - -
49D VAL* 4.0 18.8 - - + -
80D PHE* 4.0 4.9 - - - -
81D LYS* 2.8 39.1 + - + +
82D GLU* 3.0 24.2 + - - +
84D ILE* 4.2 25.4 - - + -
91D ALA* 4.5 3.6 - - + +
92D ILE* 1.3 75.6 - - - +
94D MET* 1.3 65.9 + - - +
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Residues in contact with MET 94 (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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32D PHE* 4.4 17.9 - - + -
47D VAL* 3.5 5.7 - - - +
48D ALA* 2.9 33.6 + - + +
49D VAL 5.5 0.2 - - - -
50D LYS* 4.2 13.9 - - + +
69D HIS* 3.9 22.7 - - + -
78D VAL* 4.9 2.7 - - + -
79D ARG 3.5 13.7 - - - +
80D PHE* 4.3 1.8 - - + -
81D LYS* 3.9 9.9 - - - +
92D ILE* 3.8 28.0 - - + +
93D VAL* 1.3 75.2 - - - +
95D GLU* 1.3 77.0 + - - +
96D TYR 3.5 0.2 + - - -
161D PHE* 4.3 19.7 - - + -
163D TYR* 3.7 27.1 - - + +
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Residues in contact with GLU 95 (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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32D PHE* 4.0 4.7 - - - -
45D GLU* 4.3 12.0 - - - +
46D LEU 4.8 1.3 - - - -
47D VAL* 4.8 2.9 - - - -
77D ILE 3.3 2.4 - - - +
78D VAL* 3.6 17.4 - - + +
79D ARG* 3.1 63.3 + - - +
81D LYS* 4.0 23.8 + - - +
94D MET* 1.3 89.7 - - - +
96D TYR* 1.3 61.9 + - - +
97D ALA 4.1 0.4 - - - -
157D LYS* 3.1 29.7 + - + +
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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