Contacts of the helix formed by residues 88 - 97 (chain B) in PDB entry 6DWN
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 GLY 88 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72B ASP* 3.2 18.3 + - - -
87B SER* 1.3 87.5 - - - +
89B LEU* 1.3 64.9 + - - -
90B ASP 3.6 1.6 - - - -
91B THR 4.1 1.8 - - - -
92B ILE* 3.1 18.4 + - - +
413B GLN* 3.0 19.7 + - - -
414B ILE* 3.9 5.2 - - - -
417B ASP* 4.8 5.8 - - - -
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Residues in contact with LEU 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLY* 1.3 71.1 - - - +
90B ASP* 1.3 67.5 + - - +
92B ILE* 3.4 1.7 + - - +
93B ARG* 3.0 44.8 + - - +
414B ILE* 3.9 10.5 - - + +
417B ASP* 5.4 0.2 + - - -
420B LEU* 3.9 29.0 - - + +
446B LYS* 3.6 44.2 - - + +
448B ILE* 3.8 14.8 - - + -
452B MET* 3.5 28.3 - - + -
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Residues in contact with ASP 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLY 3.6 0.2 - - - -
89B LEU* 1.3 80.8 - - - +
91B THR* 1.3 52.5 + - - +
93B ARG* 3.3 10.1 + - - +
94B GLN* 2.7 35.3 + - - +
98B ARG* 3.1 22.4 + - - -
397B LYS* 3.4 22.9 + - - +
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Residues in contact with THR 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ASP* 2.8 36.9 + - + +
73B VAL* 3.8 21.8 - - + -
86B LEU* 4.9 2.9 - - + -
87B SER 3.4 14.8 - - - +
88B GLY 3.7 1.2 + - - -
89B LEU 3.3 0.6 - - - -
90B ASP* 1.3 79.2 - - - +
92B ILE* 1.3 61.1 + - - +
94B GLN* 3.3 4.8 + - - +
95B ALA* 3.2 21.1 + - - +
396B LEU* 4.0 8.3 - - + +
397B LYS* 3.3 36.7 + - + +
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Residues in contact with ILE 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LEU* 3.5 39.3 - - + +
87B SER* 3.7 12.1 - - - +
88B GLY 3.1 20.2 + - - +
89B LEU 4.0 2.2 - - - +
91B THR* 1.3 74.1 - - - +
93B ARG* 1.3 61.9 + - - +
95B ALA* 3.0 5.2 + - - -
96B LEU* 2.9 54.5 + - + +
409B VAL* 3.7 18.6 - - + -
410B ASN 4.2 4.7 - - - +
414B ILE* 3.4 25.4 - - + -
448B ILE* 5.8 2.0 - - + -
452B MET* 3.9 12.6 - - + -
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Residues in contact with ARG 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B LEU* 3.0 49.5 + - - +
90B ASP* 3.7 9.2 + - - +
92B ILE* 1.3 77.5 - - - +
94B GLN* 1.3 62.2 + - - +
97B VAL* 3.1 45.8 + - + +
98B ARG* 3.4 21.7 + - - +
445B GLU* 3.5 26.1 + - - +
446B LYS* 6.1 0.6 - - - +
448B ILE* 4.2 0.8 - - - +
452B MET* 3.6 25.0 - - - +
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Residues in contact with GLN 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ASP* 2.7 24.5 + - - +
91B THR* 3.3 10.5 - - - +
92B ILE 3.1 0.2 - - - -
93B ARG* 1.3 74.7 - - - +
95B ALA* 1.3 57.5 + - - +
98B ARG* 2.6 46.2 + - - +
99B GLN* 2.9 50.4 + - - +
396B LEU* 3.6 18.8 - - + -
397B LYS* 5.0 9.9 - - + +
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LEU* 4.0 15.3 - - + -
91B THR 3.2 6.4 + - - +
92B ILE 3.0 4.4 + - - +
94B GLN* 1.3 79.9 - - - +
96B LEU* 1.3 61.0 + - + +
99B GLN* 2.9 31.0 - - - +
100B GLY* 3.5 0.5 - - - -
103B PHE* 3.3 25.5 - - + -
396B LEU* 3.6 34.3 - - + -
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Residues in contact with LEU 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B LEU* 5.3 2.9 - - + -
92B ILE* 2.9 36.8 + - + +
95B ALA* 1.3 81.3 - - + +
97B VAL* 1.3 60.0 + - - +
100B GLY* 2.8 19.6 - - - -
103B PHE* 4.1 22.2 - - + +
385B THR* 5.4 2.5 - - + -
388B HIS* 4.4 29.8 - - + +
407B VAL* 6.5 0.2 - - + -
409B VAL* 4.2 21.5 - - + -
451B GLY 5.1 0.4 - - - -
452B MET* 3.9 37.9 - - + +
453B GLY* 3.1 16.4 - - - -
454B LYS* 4.1 1.0 + - - +
601B HEM 5.0 2.2 - - - +
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ARG* 3.1 33.6 + - + +
96B LEU* 1.3 77.9 - - - +
98B ARG* 1.3 75.0 + - + +
99B GLN 3.2 1.1 - - - -
100B GLY* 3.1 10.7 + - - -
452B MET* 3.9 23.1 - - + -
453B GLY* 3.9 11.2 - - - +
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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