Contacts of the helix formed by residues 80 - 88 (chain D) in PDB entry 3Q37
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 SER 80 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C CYS* 3.3 13.1 - - - -
69D ILE* 3.4 8.3 - - - -
71D ARG 3.7 7.0 - - - -
72D SER* 2.7 44.7 + - - -
79D VAL* 1.3 77.3 - - - +
81D LEU* 1.3 65.6 + - - +
82D GLN* 3.5 3.7 + - - -
83D ILE* 3.2 17.5 + - - +
84D LEU* 3.1 25.2 + - - +
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Residues in contact with LEU 81 (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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68D ALA* 3.6 19.9 - - + +
69D ILE 3.1 17.3 + - - +
70D THR* 4.1 6.7 - - - +
80D SER* 1.3 72.4 - - - +
82D GLN* 1.3 63.0 + - - +
84D LEU* 3.3 3.1 + - - -
85D LYS* 2.9 30.4 + - - +
92D VAL* 4.6 4.3 - - + -
94D LEU* 5.7 1.3 - - + -
113D LYS* 4.4 3.4 - - + +
116D ALA* 3.5 22.2 - - + +
117D ALA* 3.4 45.1 - - + +
120D SER* 4.4 10.1 - - - +
122D PHE* 3.5 32.8 - - + -
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Residues in contact with GLN 82 (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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70D THR 3.1 27.2 + - - +
71D ARG* 3.7 11.5 - - - +
72D SER* 3.8 12.5 + - - +
80D SER* 3.1 11.9 - - - +
81D LEU* 1.3 80.7 + - - +
83D ILE* 1.3 58.5 + - + +
85D LYS* 3.4 8.1 + - - +
86D ASP* 3.0 28.2 + - - +
120D SER* 4.4 14.4 + - - +
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Residues in contact with ILE 83 (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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15C CYS* 3.8 10.8 - - - -
16C ASN* 3.7 34.3 - - - +
17C GLY 3.5 17.3 - - - +
45C THR* 4.0 15.3 - - + +
47C LEU* 3.5 27.2 - - + +
48C HIS* 3.6 17.0 + - + +
72D SER* 3.8 6.1 - - - +
79D VAL* 3.9 10.3 - - + -
80D SER* 3.2 22.5 + - - +
82D GLN* 1.3 75.8 - - + +
84D LEU* 1.3 65.3 + - - +
86D ASP* 3.4 8.9 + - - +
87D TYR* 3.2 17.0 + - - +
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Residues in contact with LEU 84 (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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47C LEU* 4.0 21.1 - - + -
46D PHE* 4.5 1.6 - - + -
49D ILE* 4.2 14.6 - - + -
65D ALA* 3.6 34.1 - - + -
67D ASN 4.0 1.8 - - - +
68D ALA* 3.8 26.7 - - + -
79D VAL* 3.8 13.9 - - + -
80D SER 3.1 12.6 + - - +
81D LEU* 3.6 7.4 - - - +
83D ILE* 1.3 77.1 - - - +
85D LYS* 1.3 62.2 + - - +
87D TYR* 3.0 10.2 + - - +
88D GLY 3.1 0.3 + - - -
89D ILE* 3.0 35.6 + - + +
92D VAL* 5.0 0.9 - - + -
122D PHE* 4.0 16.2 - - + -
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Residues in contact with LYS 85 (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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81D LEU 2.9 16.5 + - - +
82D GLN* 3.7 8.3 - - - +
83D ILE 3.3 0.2 - - - -
84D LEU* 1.3 76.0 - - - +
86D ASP* 1.3 58.1 + - - +
88D GLY* 3.0 19.4 + - - -
89D ILE 3.8 11.6 + - - +
120D SER* 3.2 39.8 + - - +
121D GLY* 5.3 0.4 - - - -
122D PHE* 4.1 8.0 - - + -
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Residues in contact with ASP 86 (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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17C GLY 4.9 0.6 - - - +
18C SER* 3.5 25.5 - - - -
19C GLN* 2.9 43.7 + - - +
20C GLN* 4.7 6.2 - - - +
48C HIS* 4.9 1.6 + - - -
82D GLN 3.0 17.9 + - - +
83D ILE* 3.6 8.7 - - - +
84D LEU 3.3 0.2 - - - -
85D LYS* 1.3 76.4 - - - +
87D TYR* 1.3 61.5 + - - +
88D GLY* 3.2 0.9 + - - -
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Residues in contact with TYR 87 (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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19C GLN* 3.5 45.7 + - + +
47C LEU* 3.8 40.9 + - + -
48C HIS* 4.2 13.7 - + - -
51C MET* 4.1 20.8 + - - +
49D ILE* 5.1 7.0 - - + -
50D PRO* 3.8 40.9 - - + +
53D LYS* 3.7 24.6 - - + +
83D ILE 3.2 4.0 + - - +
84D LEU 3.0 10.0 + - - +
86D ASP* 1.3 76.8 - - - +
88D GLY* 1.3 61.0 + - - +
89D ILE* 3.5 6.3 - - + +
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Residues in contact with GLY 88 (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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53D LYS* 3.2 24.2 + - - -
85D LYS 3.0 14.1 + - - -
86D ASP 3.2 1.4 - - - -
87D TYR* 1.3 80.4 - - - +
89D ILE* 1.3 65.0 + - - +
90D SER* 3.9 5.0 + - - -
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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