Contacts of the strand formed by residues 67 - 73 (chain D) in PDB entry 2UUG
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 PRO 67 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7D ILE* 4.0 27.8 - - + -
57D LEU* 4.5 7.0 - - + -
58D LEU 3.8 6.7 - - - +
59D THR* 4.1 7.2 - - + -
65D TYR 3.1 10.9 - - - +
66D LYS* 1.3 117.3 + - + +
68D TRP* 1.3 59.5 + - - +
84D LEU* 3.8 32.9 - - + +
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Residues in contact with TRP 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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29D VAL* 4.3 4.7 - - + -
33D ILE* 3.5 33.0 - - + -
35D ASN* 3.3 33.6 + - + -
37D PRO* 3.7 30.9 - - + +
41D ILE* 4.3 17.3 - - + -
58D LEU* 2.9 36.1 + - + +
59D THR* 5.0 1.3 - - - -
60D SER* 6.3 0.2 - - - -
66D LYS 4.2 5.6 - - - +
67D PRO* 1.3 75.6 - - - +
69D ALA* 1.3 79.9 + - + +
83D MET* 3.7 20.4 - - + +
84D LEU* 3.3 31.7 + - - +
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Residues in contact with ALA 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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33D ILE* 4.6 16.4 - - + -
57D LEU* 3.5 12.0 - - - +
58D LEU* 3.3 34.4 + - + -
68D TRP* 1.3 100.9 - - + +
70D LEU* 1.3 65.3 + - - +
71D VAL* 5.2 0.9 - - + -
81D ILE* 5.0 1.8 - - + -
82D LYS 3.4 13.0 - - - +
83D MET* 4.9 0.9 - - - -
84D LEU* 4.1 8.3 - - - +
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Residues in contact with LEU 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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7D ILE* 5.4 8.3 - - + +
8D ILE* 5.7 7.9 - - + +
11D GLU* 3.3 38.6 - - + +
12D THR* 6.0 1.3 - - - +
55D VAL* 4.2 17.5 - - + -
56D MET 3.0 31.0 - - - +
57D LEU* 4.4 11.7 - - + +
58D LEU* 4.9 0.4 - - - -
69D ALA* 1.3 79.7 - - - +
71D VAL* 1.3 64.4 + - - +
72D ILE* 4.7 8.5 - - + +
80D LYS 3.5 5.2 - - - +
81D ILE* 3.6 0.3 - - - -
82D LYS* 3.0 44.3 + - + +
84D LEU* 5.2 9.9 - - + -
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Residues in contact with VAL 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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191B LEU* 4.6 12.8 - - + -
32D VAL* 5.7 1.6 - - + -
33D ILE* 5.0 8.3 - - + -
54D ASN 3.8 0.9 - - - +
55D VAL* 3.7 1.2 - - - -
56D MET* 2.8 58.4 + - + +
58D LEU* 4.2 17.2 - - + +
69D ALA* 5.2 0.2 - - + -
70D LEU* 1.3 79.4 - - - +
72D ILE* 1.3 64.7 + - - +
73D GLN 4.1 0.2 - - - -
79D ASN* 3.5 42.2 - - + +
80D LYS 4.0 4.3 - - - +
81D ILE* 4.2 22.2 - - + -
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Residues in contact with ILE 72 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D GLU* 4.3 21.5 - - + +
12D THR* 5.1 6.7 - - - +
53D GLU* 3.4 43.5 - - + +
54D ASN 3.4 6.1 - - - +
55D VAL* 4.2 20.6 - - + -
70D LEU* 4.7 8.7 - - + +
71D VAL* 1.3 81.5 - - - +
73D GLN* 1.3 60.4 + - - +
74D ASP 3.9 0.7 + - - +
78D GLU 3.3 4.7 - - - +
80D LYS* 3.2 52.7 + - + +
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Residues in contact with GLN 73 (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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190B PRO* 2.9 43.4 + - - +
191B LEU* 4.3 3.2 + - - +
194B HIS* 3.7 20.3 + - - -
53D GLU* 3.3 4.4 - - - -
54D ASN* 2.9 49.1 + - + +
56D MET* 3.7 11.9 - - + +
71D VAL 4.1 1.0 - - - -
72D ILE* 1.3 71.9 - - - +
74D ASP* 1.3 64.9 + - - +
77D GLY* 3.6 29.3 + - - -
78D GLU 3.2 4.0 - - - -
79D ASN* 3.4 24.8 + - - +
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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