Contacts of the strand formed by residues 67 - 73 (chain D) in PDB entry 3DGG
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 LYS 67 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64D PHE* 4.2 0.2 - - - -
65D LYS 5.4 1.8 - - - +
66D GLY* 1.3 71.0 - - - +
68D ALA* 1.3 59.7 + - - +
69D THR* 5.0 1.3 + - - -
82D GLU 3.5 1.4 - - - +
83D LEU* 3.3 9.4 - - - +
84D SER* 3.1 53.7 + - - +
85D SER* 3.4 29.2 + - - +
90D ASP* 5.1 0.4 + - - -
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Residues in contact with ALA 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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48D ILE* 3.8 19.5 - - + -
60D TYR* 3.5 24.3 + - + -
64D PHE* 3.8 23.1 - - + -
66D GLY 3.7 3.0 + - - -
67D LYS* 1.3 73.6 - - - +
69D THR* 1.3 65.6 + - - +
70D LEU* 5.1 1.1 - - + -
81D MET* 4.7 5.6 - - + -
82D GLU 3.3 5.6 - - - +
83D LEU* 4.1 8.3 - - + -
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Residues in contact with THR 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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60D TYR* 3.5 7.0 - - - +
67D LYS 5.0 1.9 + - - -
68D ALA* 1.3 76.4 + - - +
70D LEU* 1.3 65.2 + - - +
71D THR* 4.0 18.3 + - + +
80D TYR 3.7 0.7 - - - +
81D MET* 3.5 2.6 - - - -
82D GLU* 2.9 47.8 + - + +
84D SER* 5.6 1.7 + - - -
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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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36D TRP* 3.6 26.0 - - + -
48D ILE* 5.1 2.0 - - + -
49D GLY* 3.4 40.4 - - - +
50D TYR* 3.5 14.4 - - - +
51D ILE* 3.7 22.0 - - + +
58D THR* 3.7 12.0 - - + +
59D ASN 4.5 0.2 - - - +
60D TYR* 2.8 29.8 + - + +
68D ALA* 5.1 2.0 - - + -
69D THR* 1.3 76.3 - - - +
71D THR* 1.3 66.6 + - - +
80D TYR 3.4 2.9 - - - +
81D MET* 3.7 33.4 - - + -
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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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19D LYS* 4.4 9.8 + - - -
51D ILE* 3.3 12.8 - - - +
69D THR* 4.0 15.2 + - + +
70D LEU* 1.3 79.5 - - - +
72D SER* 1.3 67.6 + - - +
79D ALA* 3.6 3.5 - - - +
80D TYR* 2.8 48.2 + - - +
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Residues in contact with SER 72 (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 PHE* 4.2 16.6 - - - -
51D ILE* 3.5 21.5 - - - +
53D PRO* 3.8 14.2 + - - +
56D ASP* 3.7 17.3 + - - +
71D THR* 1.3 81.6 - - - +
73D ASP* 1.3 60.9 + - - +
74D LYS* 4.2 2.4 + - - +
78D THR 3.3 12.3 - - - -
79D ALA* 4.2 3.4 - - - +
80D TYR* 4.5 4.3 - - - -
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Residues in contact with ASP 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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29D PHE* 3.7 3.4 - - - -
72D SER* 1.3 74.2 - - - +
74D LYS* 1.3 62.9 - - - +
75D SER* 2.5 29.5 + - - -
76D SER* 2.7 31.4 + - - +
77D SER* 3.0 18.7 + - - -
78D THR 2.8 17.7 + - - +
80D TYR* 4.3 11.6 - - + +
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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