Contacts of the helix formed by residues 88 - 97 (chain A) in PDB entry 6DWM
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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A ASP* 3.6 19.0 + - - -
87A SER* 1.3 83.6 - - - +
89A LEU* 1.3 64.7 + - - -
90A ASP 3.4 2.0 - - - -
91A THR 4.0 1.6 - - - -
92A ILE* 3.1 19.0 + - - +
413A GLN* 2.8 22.4 + - - -
414A ILE* 4.0 4.5 - - - -
417A ASP* 5.0 5.2 - - - -
419A LYS* 6.5 0.4 - - - -
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Residues in contact with LEU 89 (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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88A GLY* 1.3 71.8 - - - +
90A ASP* 1.3 65.2 + - - +
92A ILE* 4.2 1.2 - - - +
93A ARG* 3.2 23.1 + - + +
414A ILE* 4.0 12.3 - - + +
417A ASP* 5.6 0.8 + - - -
420A LEU* 4.2 25.8 - - + +
445A GLU 5.2 1.6 - - - +
446A LYS* 3.6 44.2 - - + +
448A ILE* 3.7 33.0 - - + -
452A MET* 3.8 13.4 - - + +
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Residues in contact with ASP 90 (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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72A ASP* 5.7 0.2 + - - -
88A GLY 3.4 0.2 - - - -
89A LEU* 1.3 78.3 - - - +
91A THR* 1.3 60.5 + - - +
93A ARG* 3.3 6.0 + - - +
94A GLN* 2.8 29.1 + - - +
98A ARG* 2.9 25.9 + - - -
397A LYS* 3.1 28.2 + - - +
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Residues in contact with THR 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 2.8 31.1 + - + +
73A VAL* 3.8 29.4 - - + -
86A LEU* 4.9 2.7 - - + -
87A SER 3.3 15.9 - - - +
88A GLY 3.6 1.0 + - - -
89A LEU 3.4 0.4 - - - -
90A ASP* 1.3 77.2 - - - +
92A ILE* 1.3 62.2 + - - +
94A GLN* 3.2 4.0 + - - +
95A ALA* 3.2 21.5 + - - +
396A LEU* 4.0 9.0 - - + +
397A LYS* 3.5 35.5 + - + +
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Residues in contact with ILE 92 (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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86A LEU* 3.5 37.2 - - + +
87A SER* 3.8 12.3 - - - +
88A GLY 3.1 14.8 + - - +
89A LEU 4.2 2.7 - - - +
91A THR* 1.3 73.9 - - - +
93A ARG* 1.3 62.3 + - - +
95A ALA* 3.2 3.8 + - - -
96A LEU* 2.9 43.5 + - + +
409A VAL* 3.7 28.3 - - + -
410A ASN 4.0 7.0 - - - +
414A ILE* 3.5 26.9 - - + -
448A ILE* 5.8 2.0 - - + -
452A MET* 4.0 15.0 - - + -
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Residues in contact with ARG 93 (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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89A LEU* 3.2 22.3 + - + +
90A ASP* 3.3 6.7 + - - +
92A ILE* 1.3 76.7 - - - +
94A GLN* 1.3 62.6 + - - +
97A VAL* 3.1 57.5 + - + +
98A ARG* 3.3 28.1 + - - +
452A MET* 3.6 27.4 - - + +
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Residues in contact with GLN 94 (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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90A ASP* 2.8 16.5 + - - +
91A THR* 3.4 13.2 - - - +
92A ILE 3.2 0.2 - - - -
93A ARG* 1.3 77.9 - - - +
95A ALA* 1.3 56.2 + - - +
98A ARG* 2.8 44.0 + - - +
99A GLN* 2.8 60.8 + - - +
396A LEU* 3.7 11.9 - - + -
397A LYS* 4.6 15.4 - - + +
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Residues in contact with ALA 95 (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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86A LEU* 3.9 15.7 - - + -
91A THR 3.2 11.3 + - - +
92A ILE 3.2 2.4 + - - +
94A GLN* 1.3 78.4 - - - +
96A LEU* 1.3 60.9 + - + +
99A GLN* 3.1 30.0 - - - +
100A GLY* 3.3 0.9 + - - -
103A PHE* 3.3 28.8 - - + -
396A LEU* 3.6 28.7 - - + -
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Residues in contact with LEU 96 (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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86A LEU* 5.4 1.1 - - + -
92A ILE* 2.9 36.6 + - + +
95A ALA* 1.3 80.7 - - + +
97A VAL* 1.3 58.9 + - - +
100A GLY* 3.1 16.7 - - - -
103A PHE* 4.1 17.5 - - + +
385A THR* 5.2 2.7 - - + -
388A HIS* 3.9 29.2 - - + +
407A VAL* 6.4 0.2 - - + -
409A VAL* 4.1 24.9 - - + -
451A GLY* 5.2 0.7 - - - -
452A MET* 3.8 37.2 - - + +
453A GLY* 3.2 16.2 - - - -
454A LYS 3.9 2.9 + - - -
601A HEM 4.8 7.9 - - - +
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Residues in contact with VAL 97 (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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93A ARG* 3.1 49.1 + - + +
96A LEU* 1.3 79.5 - - - +
98A ARG* 1.3 73.6 + - + +
99A GLN 3.2 1.3 - - - -
100A GLY* 3.0 12.3 + - - -
452A MET* 3.8 24.2 - - + -
453A GLY* 4.0 11.7 - - - +
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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