Contacts of the strand formed by residues 70 - 75 (chain D) in PDB entry 3Q3G
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 ALA 70 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D ILE* 3.4 32.8 - - + -
62D TYR* 3.3 21.3 - - + -
66D PHE* 2.9 18.8 + - + +
67D GLN* 5.6 1.9 + - - -
68D GLY 4.9 3.8 + - - -
69D LYS* 1.3 75.5 + - - +
71D THR* 1.3 66.9 + - - +
83D LEU* 3.7 12.6 - - + -
84D GLN 3.3 4.0 - - - -
85D LEU* 4.2 7.4 - - + -
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Residues in contact with THR 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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21D LYS* 6.0 0.3 - - - -
62D TYR* 3.5 7.6 - - - +
68D GLY 5.5 1.9 + - - -
69D LYS 4.9 1.9 + - - -
70D ALA* 1.3 76.2 + - - +
72D ILE* 1.3 63.2 + - - +
73D THR* 4.0 20.0 + - + +
82D TYR 3.9 1.0 - - - +
83D LEU* 3.6 1.2 + - - -
84D GLN* 2.8 57.0 + - + +
86D SER* 5.6 1.2 + - - -
197H SER* 6.4 2.5 - - - -
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Residues in contact with ILE 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D TRP* 3.6 29.2 - - + +
50D ILE* 4.3 3.6 - - + -
51D GLY* 3.4 43.5 - - - +
52D ARG 3.7 2.9 - - - +
53D ILE* 3.6 33.8 - - + +
60D THR* 3.4 21.9 - - + +
62D TYR* 2.9 28.0 + - + +
71D THR* 1.3 75.2 - - - +
73D THR* 1.4 65.7 + - - +
82D TYR 3.3 12.8 - - - +
83D LEU* 3.9 11.7 - - + -
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Residues in contact with THR 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LYS* 4.0 4.6 - - - -
53D ILE* 3.6 9.8 - - - +
71D THR* 4.0 19.2 + - + +
72D ILE* 1.4 78.9 - - - +
74D ALA* 1.3 59.0 + - - +
81D ALA* 3.5 4.2 - - - +
82D TYR* 2.7 45.3 + - - +
702D GOL 3.9 17.5 - - - +
197H SER* 6.5 0.9 - - - -
198H PRO* 5.8 4.0 - - + -
202H GLU* 2.8 26.4 + - - +
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Residues in contact with ALA 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D ILE* 3.9 7.0 - - + -
53D ILE* 3.6 17.9 - - + +
55D PRO* 3.7 33.4 - - + +
58D ASP* 3.9 7.2 + - - +
73D THR* 1.3 77.0 - - - +
75D ASP* 1.3 56.5 + - - +
76D THR* 4.0 1.5 + - + -
80D THR 3.5 5.2 - - - +
81D ALA* 4.6 2.2 - - - -
82D TYR* 4.5 0.7 - - - -
614D EDO 4.3 0.6 - - - -
702D GOL 2.7 36.4 + - - -
202H GLU* 4.1 2.0 - - - -
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Residues in contact with ASP 75 (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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31D ILE* 3.8 1.8 - - - -
74D ALA* 1.3 71.6 - - - +
76D THR* 1.3 60.4 + - - +
77D SER* 3.4 10.7 - - - -
78D SER* 2.6 26.3 + - - +
79D ASN 2.9 22.2 + - - -
80D THR 2.7 18.5 + - - -
82D TYR* 3.6 22.5 + - + -
614D EDO 2.4 27.7 + - - -
702D GOL 3.5 8.3 - - - +
202H GLU* 3.9 2.1 - - + -
203H THR* 3.0 34.6 + - - -
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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