Contacts of the helix formed by residues 67 - 73 (chain D) in PDB entry 3GV5
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 ASN 67 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37D CYS* 4.0 8.5 - - - -
40D ALA* 3.9 6.0 - - + +
44D MSE 3.7 38.9 - - + -
50D LEU 4.2 0.8 + - - -
51D LYS 4.7 4.0 + - - -
53D LYS 2.7 25.4 + - - -
54D PRO* 3.7 0.2 - - - +
55D LEU* 2.9 38.3 + - + +
66D CYS* 1.3 76.5 - - - +
68D TYR* 1.3 67.5 + - - +
69D GLU* 4.0 7.0 - - - +
70D ALA* 3.0 15.1 + - - +
71D ARG* 3.1 18.5 + - - +
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Residues in contact with TYR 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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36D ASP* 4.3 4.4 + - + -
37D CYS* 4.0 22.9 - - + -
67D ASN* 1.3 76.5 - - - +
69D GLU* 1.3 60.4 + - - +
71D ARG* 3.2 31.7 + - + +
72D LYS* 3.0 39.4 + - - +
214D LYS* 3.3 25.7 - - + +
215D PRO* 3.7 50.1 - - + +
424D ADI 2.7 28.0 + - - -
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Residues in contact with GLU 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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51D LYS 4.9 1.4 - - - +
52D ASP* 3.0 28.5 - - - +
53D LYS 3.1 11.6 - - - +
54D PRO* 3.6 22.1 - - - +
67D ASN* 3.2 10.8 + - - +
68D TYR* 1.3 77.1 - - - +
70D ALA* 1.3 62.0 + - - +
72D LYS* 3.4 16.0 + - + +
73D LEU* 3.3 34.9 + - + +
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Residues in contact with ALA 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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54D PRO* 3.9 8.6 - - - +
55D LEU 3.7 7.0 - - - +
66D CYS* 3.7 20.6 - - + -
67D ASN* 3.0 23.5 + - - +
69D GLU* 1.3 76.0 - - - +
71D ARG* 1.3 59.9 + - - +
73D LEU* 3.2 9.6 + - - -
74D GLY 3.4 0.2 + - - -
75D VAL* 3.0 31.9 + - + +
91D LEU* 3.7 20.4 - - + -
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Residues in contact with ARG 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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49B GLU* 3.6 27.5 - - + +
37D CYS* 3.6 5.1 - - - +
65D THR* 3.2 20.8 + - - -
66D CYS* 3.1 30.1 + - - +
67D ASN 3.1 13.9 + - - +
68D TYR* 3.2 48.3 + - + +
70D ALA* 1.3 73.9 - - - +
72D LYS* 1.3 65.5 + - + +
74D GLY* 3.0 14.9 + - - -
75D VAL 3.4 13.8 + - - +
76D LYS* 5.7 0.4 - - - -
77D LYS* 3.9 20.8 - - + +
214D LYS* 4.4 4.0 - - - +
424D ADI 3.0 41.8 + - - -
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Residues in contact with LYS 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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46B SER 3.8 17.4 - - - +
47B ASN* 3.4 45.5 + - + +
48B PRO* 4.1 10.2 - - - +
49B GLU* 4.5 1.7 - - + +
68D TYR* 3.0 27.9 + - - +
69D GLU* 3.5 17.5 - - + +
71D ARG* 1.3 76.0 - - - +
73D LEU* 1.3 61.6 + - + +
74D GLY* 3.1 5.0 + - - -
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Residues in contact with LEU 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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46B SER 5.5 4.3 - - - +
54D PRO* 4.0 20.9 - - + -
69D GLU* 3.3 27.6 + - + +
70D ALA 3.2 7.3 + - - +
71D ARG 3.2 1.2 - - - -
72D LYS* 1.3 77.2 - - + +
74D GLY* 1.3 57.2 + - - +
75D VAL* 3.5 2.8 + - - -
87D LYS* 3.1 33.5 - - - +
88D CYS* 4.1 13.5 - - - +
90D GLN* 4.0 23.8 - - - +
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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