Contacts of the helix formed by residues 57 - 65 (chain D) in PDB entry 6B0B
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 57 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56D PHE* 1.3 90.5 - - - +
58D TRP* 1.3 63.2 + - - +
59D ASP* 4.2 7.4 - - + +
60D ILE* 3.3 19.1 - - + +
135D VAL* 3.4 30.1 + - + +
138D LYS* 4.5 13.2 - - + -
140D THR* 4.1 22.2 - - + +
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Residues in contact with TRP 58 (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 ILE* 3.6 31.2 - - + -
46D LEU* 3.7 38.4 - - + -
48D VAL* 4.5 6.5 - - + -
54D LEU* 3.8 22.7 - - + -
56D PHE* 3.5 4.5 + - - -
57D ALA* 1.3 68.5 - - - +
59D ASP* 1.3 64.0 + - - +
60D ILE 3.1 3.6 - - - -
61D LEU* 2.9 38.2 + - + +
62D SER* 3.6 2.4 + - - +
65D PHE* 4.7 7.9 - + - -
201D ILE* 4.3 12.8 - - + -
208D TYR* 3.8 44.3 - + + +
209D THR 6.0 0.4 - - - -
211D VAL* 3.4 30.8 - - + +
213D GLN* 2.7 29.5 + - - -
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Residues in contact with ASP 59 (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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57D ALA* 3.2 4.9 - - + +
58D TRP* 1.3 81.4 - - - +
60D ILE* 1.3 58.0 + - + +
61D LEU 3.1 0.2 - - - -
62D SER* 2.8 18.3 + - - -
63D PRO* 3.2 1.0 - - - +
140D THR* 3.0 27.3 + - - +
142D GLY* 3.5 27.4 + - - -
143D TRP* 2.7 36.9 + - + +
165D LEU* 4.6 8.5 - - + -
201D ILE* 4.3 19.1 - - - +
208D TYR* 5.5 5.6 - - - -
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Residues in contact with ILE 60 (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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22D VAL* 4.8 8.5 - - + -
56D PHE* 3.5 28.3 - - + -
57D ALA* 3.3 18.6 - - + +
59D ASP* 1.3 76.5 - - + +
61D LEU* 1.3 72.3 + - + +
63D PRO* 3.8 3.3 - - - +
64D GLN* 3.3 22.3 + - - +
97D MET* 4.5 4.3 - - - +
99D PHE* 4.1 28.0 - - + -
105D VAL* 4.7 20.4 - - + +
124D LEU* 5.2 3.1 - - + +
129D PHE* 4.8 5.2 - - + -
135D VAL* 4.3 26.7 - - + -
143D TRP* 4.6 8.7 - - + -
165D LEU* 5.4 3.8 - - + -
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Residues in contact with LEU 61 (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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18D MET* 4.6 10.6 - - + +
27D PHE* 4.5 4.5 - - + -
29D ILE* 3.7 29.2 - - + -
54D LEU* 4.1 2.5 - - + -
56D PHE* 4.1 21.8 - - + -
58D TRP* 2.9 35.9 + - + +
60D ILE* 1.3 95.9 - - + +
62D SER* 1.3 63.1 + - - +
63D PRO* 3.5 1.8 - - - -
64D GLN* 3.3 19.0 + - + +
65D PHE* 3.4 20.1 - - + -
124D LEU* 3.6 33.2 - - + -
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Residues in contact with SER 62 (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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58D TRP* 3.6 4.4 + - - -
59D ASP* 2.8 27.3 + - - -
61D LEU* 1.3 72.6 - - - +
63D PRO* 1.3 61.7 - - - +
64D GLN 3.0 11.2 + - - -
65D PHE* 3.4 14.4 + - - +
143D TRP* 3.7 12.6 - - - -
199D LEU* 3.4 40.4 - - - +
201D ILE* 4.6 6.7 - - - -
213D GLN* 3.8 21.7 + - - +
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Residues in contact with PRO 63 (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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59D ASP 3.2 8.1 - - - +
60D ILE 3.8 8.1 - - - +
61D LEU 3.5 3.6 - - - -
62D SER* 1.3 96.1 - - - +
64D GLN* 1.3 60.4 + - - +
65D PHE 3.4 2.1 + - - -
70D LYS* 4.1 13.2 + - - +
95D ARG* 2.4 38.0 + - - +
97D MET* 4.8 4.5 - - + -
143D TRP* 3.7 22.9 - - + +
163D GLN* 3.8 23.6 - - - +
177D VAL* 6.5 0.4 - - + -
199D LEU* 4.8 4.7 - - + -
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Residues in contact with GLN 64 (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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18D MET* 4.8 11.7 - - + -
60D ILE 3.3 12.7 + - - +
61D LEU* 3.3 23.8 - - - +
62D SER 3.0 1.8 + - - -
63D PRO* 1.3 81.5 - - - +
65D PHE* 1.3 66.8 + - + +
70D LYS* 5.9 0.6 - - - +
93D TRP* 3.1 52.0 + - + -
95D ARG* 3.3 19.7 + - - +
97D MET* 3.3 31.9 - - - -
105D VAL* 5.2 0.2 - - - +
107D VAL* 3.8 22.0 - - + +
109D GLN* 5.4 2.1 + - - +
122D VAL* 5.4 1.9 - - + +
124D LEU* 4.8 5.6 - - + -
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Residues in contact with PHE 65 (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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14D PHE* 5.2 12.3 - + + -
16D VAL* 4.2 27.4 - - + -
18D MET* 4.5 19.1 - - + -
29D ILE* 5.6 4.0 - - + -
42D GLN* 4.6 13.2 - - - +
44D ALA* 5.5 3.8 - - + -
46D LEU* 4.1 30.5 - - + -
58D TRP* 4.7 6.7 - + - -
61D LEU* 3.4 24.7 - - + -
62D SER 3.4 8.2 + - - +
63D PRO 4.2 0.7 - - - +
64D GLN* 1.3 84.4 - - - +
70D LYS* 3.4 45.8 + - - +
120D TYR* 5.8 7.0 - + - -
122D VAL* 5.9 0.7 - - + -
213D GLN* 3.3 37.7 - - - +
215D GLU* 3.9 21.5 - - - +
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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