Contacts of the helix formed by residues 88 - 102 (chain D) in PDB entry 6BCH
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 88 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87D GLU* 1.3 82.1 - - - +
89D LEU* 1.3 64.7 + - - +
90D LYS* 3.9 6.2 + - - +
91D GLU* 3.3 22.5 + - - +
92D LEU* 3.0 22.7 + - - +
5F T 3.7 20.6 - - - -
6F G 3.8 25.0 + - - -
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Residues in contact with LEU 89 (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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50D PRO* 5.0 6.7 - - + -
87D GLU 5.7 0.2 - - - +
88D SER* 1.3 72.4 - - - +
90D LYS* 1.3 56.9 + - - +
92D LEU* 3.5 0.4 + - - -
93D GLU* 2.9 28.6 + - - +
119D PHE* 3.6 35.2 - - + -
122D ILE* 4.3 23.6 - - + +
123D LYS* 4.7 18.6 - - + +
4F A 4.6 12.6 - - - +
5F T 3.0 34.2 + - - +
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Residues in contact with LYS 90 (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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88D SER* 3.3 6.6 + - - +
89D LEU* 1.3 77.9 - - - +
91D GLU* 1.3 56.7 + - - +
93D GLU* 3.2 9.3 - - - +
94D VAL* 3.0 31.9 + - - +
5F T 4.8 0.4 + - - -
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Residues in contact with GLU 91 (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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73D ALA* 4.7 10.3 - - + -
74D GLY* 5.0 3.4 - - - +
86D PHE* 3.8 31.3 - - + -
87D GLU 4.6 0.4 - - - +
88D SER* 3.3 20.7 + - - +
90D LYS* 1.3 76.8 - - - +
92D LEU* 1.3 66.2 + - - +
94D VAL* 3.0 12.1 + - - +
95D VAL* 2.9 23.7 + - - +
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Residues in contact with LEU 92 (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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50D PRO* 3.5 46.2 - - + +
52D PHE* 3.7 17.5 - - + +
86D PHE* 3.2 26.2 - - + +
87D GLU 3.7 14.1 - - - +
88D SER 3.0 16.3 + - - +
89D LEU* 5.0 0.7 - - - -
91D GLU* 1.3 76.3 - - - +
93D GLU* 1.3 57.9 + - - +
95D VAL* 3.1 5.9 + - + +
96D ILE* 2.9 38.7 + - + +
115D PHE* 3.6 21.8 - - + -
119D PHE* 3.9 17.7 - - + -
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Residues in contact with GLU 93 (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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89D LEU 2.9 15.3 + - - +
90D LYS* 3.2 14.1 - - - +
91D GLU 3.1 0.4 - - - -
92D LEU* 1.3 77.0 - - - +
94D VAL* 1.3 57.4 + - + +
96D ILE* 3.4 5.8 + - - +
97D ASN* 2.9 29.8 + - - +
119D PHE* 4.2 14.8 - - + -
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Residues in contact with VAL 94 (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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71D LEU* 4.2 40.4 - - + +
73D ALA* 4.5 13.7 - - + -
86D PHE* 5.5 0.4 - - + -
90D LYS* 3.0 17.8 + - + +
91D GLU* 3.2 11.0 - - - +
93D GLU* 1.3 77.6 - - + +
95D VAL* 1.3 57.4 + - + +
97D ASN* 3.3 7.2 + - - +
98D HIS* 3.0 27.2 + - - +
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Residues in contact with VAL 95 (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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32D PHE* 4.4 6.3 - - + -
52D PHE* 3.8 24.7 - - + -
71D LEU* 5.4 4.5 - - + -
86D PHE* 3.5 38.1 - - + -
91D GLU 2.9 16.8 + - - +
92D LEU* 3.4 11.7 - - + +
94D VAL* 1.3 73.9 - - - +
96D ILE* 1.3 62.6 + - + +
98D HIS* 3.1 8.2 + - - +
99D PHE* 2.9 55.3 + - + -
112D TYR* 5.0 1.6 - - + -
115D PHE* 5.6 1.6 - - + -
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Residues in contact with ILE 96 (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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92D LEU 2.9 27.3 + - - +
93D GLU* 3.8 4.3 - - - +
95D VAL* 1.3 75.4 - - + +
97D ASN* 1.3 58.6 + - - +
100D ASP* 2.9 47.7 + - - +
112D TYR* 3.0 30.9 + - + +
115D PHE* 4.2 16.6 - - + -
116D LYS* 4.8 11.2 - - + -
119D PHE* 3.5 42.4 - - + -
120D TYR* 4.8 17.9 - - + +
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Residues in contact with ASN 97 (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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93D GLU 2.9 18.7 + - - +
94D VAL* 3.6 7.9 - - - +
95D VAL 3.2 0.2 - - - -
96D ILE* 1.3 76.4 - - - +
98D HIS* 1.3 62.6 + - - +
100D ASP* 3.4 7.4 + - - +
101D LYS* 3.0 23.7 + - - +
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Residues in contact with HIS 98 (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 PRO* 3.6 28.7 + - + -
22D ILE* 3.8 19.0 - - + +
23D THR* 3.3 15.7 + - - -
70D TYR* 4.2 17.4 - + - -
71D LEU* 4.2 17.1 - - + +
94D VAL 3.0 13.8 + - - +
95D VAL* 3.1 9.8 + - - +
97D ASN* 1.3 77.6 - - - +
99D PHE* 1.3 76.6 + + - +
101D LYS* 2.9 6.2 + - - +
102D TYR* 2.6 57.0 + + - +
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Residues in contact with PHE 99 (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 ILE* 5.4 2.5 - - + -
23D THR* 4.0 17.3 - - - -
26D ALA* 3.8 20.6 - - + -
32D PHE* 3.7 14.1 - + - -
52D PHE* 3.7 13.2 - + - -
95D VAL* 2.9 43.8 + - + -
98D HIS* 1.3 88.1 - + - +
100D ASP* 1.3 64.8 + - - +
102D TYR 3.7 13.9 - - - -
103D PRO* 3.1 28.8 - - + +
104D LEU* 3.5 35.7 - - + +
112D TYR* 3.6 33.9 - + + +
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Residues in contact with ASP 100 (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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96D ILE* 2.9 35.8 + - - +
97D ASN* 3.6 7.5 - - - +
99D PHE* 1.3 79.4 - - - +
101D LYS* 1.3 59.6 + - - +
103D PRO* 4.1 8.5 - - - +
112D TYR* 3.0 22.1 + - - -
120D TYR* 5.5 1.2 + - - -
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Residues in contact with LYS 101 (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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20D TRP* 4.7 2.4 - - - -
97D ASN 3.0 15.7 + - - +
98D HIS* 2.9 5.6 + - - +
100D ASP* 1.3 79.6 - - - +
102D TYR* 1.3 85.7 + - + +
103D PRO* 3.4 7.4 - - - +
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Residues in contact with TYR 102 (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 PRO* 3.4 35.4 - - + +
20D TRP* 3.7 36.1 - + + -
23D THR* 2.6 36.5 + - - +
70D TYR* 4.2 8.9 + - - -
98D HIS* 2.6 34.1 + - + +
99D PHE* 3.5 11.4 - - - -
101D LYS* 1.3 96.0 - - + +
103D PRO* 1.3 63.0 - - - +
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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