Contacts of the helix formed by residues 67 - 74 (chain A) in PDB entry 3Q29
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 ARG 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A GLU* 3.9 27.7 + - - +
46A GLU* 5.2 2.4 - - - +
63A TRP* 3.1 32.3 - - + +
64A ALA 3.5 0.9 + - - +
65A HIS 3.2 0.8 - - - -
66A ASP* 1.3 80.1 + - - +
68A PHE* 1.3 64.6 + - + +
69A GLY 3.3 0.2 - - - -
70A GLY* 3.1 14.0 + - - -
71A TYR* 3.3 45.4 + - + +
337A MET* 6.0 0.4 - - - -
338A SER* 3.2 31.6 + - - +
341A TRP* 3.7 23.4 - - - +
342A TYR* 5.0 11.7 + - - -
2B GLC 2.8 37.9 + - - +
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Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ILE* 3.5 28.7 - - + -
63A TRP* 3.1 36.3 - - + -
64A ALA 3.4 13.9 - - - -
65A HIS* 3.0 17.7 + - + +
67A ARG* 1.3 76.5 - - + +
69A GLY* 1.3 65.0 + - - +
71A TYR* 3.6 11.7 - + - +
72A ALA* 2.9 26.9 + - - +
77A LEU* 3.3 24.3 - - + +
98A VAL* 6.1 1.6 - - + -
105A ILE* 3.6 20.0 - - + +
106A ALA* 3.9 13.0 - - + -
264A SER* 3.7 15.0 - - - -
266A GLY* 3.6 25.6 - - - -
333A ASN* 5.8 0.4 - - + +
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Residues in contact with GLY 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A HIS 4.2 2.2 + - - -
66A ASP 4.2 0.2 + - - -
68A PHE* 1.3 77.2 - - - +
70A GLY* 1.3 60.0 + - - +
72A ALA 3.6 0.2 + - - -
73A GLN* 3.2 20.6 + - - +
100A TYR* 3.6 31.8 - - - -
333A ASN* 2.8 31.8 + - - +
335A PRO* 4.2 5.4 - - - -
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Residues in contact with GLY 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GOL 6.4 0.2 - - - -
66A ASP 5.0 0.2 + - - -
67A ARG 3.1 8.3 + - - -
69A GLY* 1.3 74.3 - - - +
71A TYR* 1.3 68.4 + - - +
73A GLN* 3.5 3.1 + - - +
74A SER* 3.4 23.0 + - - -
76A LEU* 5.2 0.2 - - - +
333A ASN 4.0 0.8 + - - -
334A ILE 4.7 0.6 + - - -
335A PRO* 3.8 28.6 - - - +
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Residues in contact with TYR 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A GLU* 2.8 34.6 + - - +
48A PHE* 4.0 21.8 - + - -
49A PRO* 4.0 29.1 - - + +
61A ILE* 3.7 22.9 - - + +
63A TRP* 5.1 1.6 - - + -
67A ARG* 3.3 38.8 + - + +
68A PHE* 3.3 30.5 + + - +
70A GLY* 1.3 78.3 - - - +
72A ALA* 1.3 63.9 + - - +
74A SER 3.1 6.6 + - - -
76A LEU* 3.1 35.6 + - + +
77A LEU* 3.6 15.5 - - + -
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Residues in contact with ALA 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A PHE 2.9 17.2 + - - +
69A GLY 3.7 0.2 - - - +
71A TYR* 1.3 75.6 - - - +
73A GLN* 1.3 54.6 + - - +
75A GLY* 2.6 27.7 + - - -
76A LEU 4.7 0.7 - - - +
77A LEU* 3.9 13.0 - - + +
100A TYR* 3.6 25.8 - - + -
105A ILE* 4.1 25.1 - - + -
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Residues in contact with GLN 73 (chain A).
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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69A GLY 3.2 13.1 + - - +
70A GLY 3.9 5.2 - - - +
71A TYR 3.3 0.6 - - - -
72A ALA* 1.3 78.3 - - - +
74A SER* 1.3 57.3 + - - +
75A GLY 3.2 2.2 + - - -
100A TYR* 2.7 40.4 + - - +
101A ASN* 3.7 10.7 + - - +
335A PRO* 4.0 15.0 - - + -
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Residues in contact with SER 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLY 3.4 11.2 + - - -
71A TYR 3.1 9.0 + - - -
72A ALA 3.0 1.4 + - - -
73A GLN* 1.3 77.6 - - - +
75A GLY* 1.3 66.5 + - - +
76A LEU* 3.2 26.3 + - - +
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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