Contacts of the helix formed by residues 80 - 92 (chain A) in PDB entry 4GDK
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 THR 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A THR 4.0 9.0 - - - +
79A ARG* 1.3 82.3 - - - +
81A ILE* 1.3 64.5 + - - +
82A GLN* 3.6 3.8 + - - +
83A GLY* 3.2 18.2 + - - -
84A LEU* 3.1 22.9 + - - +
112A PRO 3.5 12.2 + - - -
113A ASP* 3.9 19.7 - - + +
114A GLN 3.4 9.4 - - - +
115A GLU* 4.2 8.3 - - + +
116A VAL* 4.2 2.6 - - - +
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Residues in contact with ILE 81 (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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80A THR* 1.3 74.6 - - - +
82A GLN* 1.3 53.0 + - - +
84A LEU* 3.0 7.9 + - + +
85A ILE* 2.7 52.4 + - + +
102A ILE* 4.1 26.7 - - + +
110A PRO* 3.8 23.8 - - + +
111A SER 3.8 8.7 - - - +
112A PRO* 3.4 17.0 + - + +
114A GLN 3.0 20.1 + - - +
116A VAL* 4.5 9.0 - - + -
119A LEU* 3.7 24.9 - - + -
131A LEU* 4.6 9.4 - - + -
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Residues in contact with GLN 82 (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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80A THR* 4.1 2.7 - - - +
81A ILE* 1.3 77.0 - - - +
83A GLY* 1.3 56.7 + - - +
85A ILE* 3.1 23.1 + - - +
86A ASP* 2.8 66.7 + - - +
89A LYS* 5.3 1.6 + - - -
112A PRO* 2.9 40.7 + - + +
113B LEU* 5.9 2.4 - - + +
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Residues in contact with GLY 83 (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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79A ARG* 3.6 22.5 + - - -
80A THR* 3.2 16.1 + - - -
82A GLN* 1.3 77.3 - - - +
84A LEU* 1.3 58.5 + - - +
86A ASP* 4.1 9.3 - - - +
87A PHE* 3.3 20.4 + - - +
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Residues in contact with LEU 84 (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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57A ILE* 3.8 20.6 - - + -
59A LEU* 5.0 5.6 - - + -
73A TRP* 6.3 0.4 - - + -
75A VAL* 4.4 15.3 - - + -
79A ARG* 4.0 18.6 - - - +
80A THR 3.1 11.5 + - - +
81A ILE* 3.0 12.4 + - + +
83A GLY* 1.3 77.8 - - - +
85A ILE* 1.3 63.7 + - - +
87A PHE* 3.3 20.2 + - + +
88A ILE* 3.1 35.0 + - + +
102A ILE* 4.5 10.8 - - + -
116A VAL* 4.3 10.1 - - + -
131A LEU* 3.6 30.5 - - + -
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Residues in contact with ILE 85 (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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81A ILE* 2.7 35.3 + - + +
82A GLN* 3.4 30.7 - - - +
84A LEU* 1.3 72.3 - - - +
86A ASP* 1.3 56.7 + - - +
88A ILE* 3.1 5.0 + - - +
89A LYS* 2.8 53.3 + - - +
100A LEU* 3.4 35.2 - - + +
102A ILE* 3.6 25.1 - - + +
112A PRO* 5.1 2.9 - - + -
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Residues in contact with ASP 86 (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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82A GLN* 2.8 43.2 + - - +
83A GLY* 4.3 6.9 - - - +
85A ILE* 1.3 76.0 - - - +
87A PHE* 1.3 65.5 + - - +
88A ILE 3.5 0.2 + - - -
89A LYS* 4.0 16.6 + - - +
90A LYS* 3.1 43.5 + - - +
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Residues in contact with PHE 87 (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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59A LEU* 5.2 0.9 - - + -
68A MET* 4.4 4.0 - - + -
73A TRP* 3.6 60.6 - + + -
79A ARG* 4.7 13.0 - - - +
83A GLY 3.3 14.2 + - - +
84A LEU* 3.4 24.0 - - + +
86A ASP* 1.3 81.2 - - - +
88A ILE* 1.3 72.8 + - + +
90A LYS* 3.8 11.6 + - - +
91A PHE* 3.5 33.1 + + - -
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Residues in contact with ILE 88 (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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59A LEU* 3.8 39.7 - - + -
68A MET* 3.9 15.7 - - + -
84A LEU* 3.2 18.4 - - + +
85A ILE 3.1 7.6 + - - +
87A PHE* 1.3 83.0 - - + +
89A LYS* 1.3 65.5 + - - +
90A LYS 3.2 2.0 - - - -
91A PHE* 2.9 13.7 + - - +
92A LEU* 3.0 37.2 + - + +
100A LEU* 3.7 11.9 - - + -
102A ILE* 4.3 19.3 - - + -
133A TYR* 4.7 14.8 - - + -
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Residues in contact with LYS 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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82A GLN* 5.3 1.8 + - - -
85A ILE* 2.8 39.1 + - + +
86A ASP* 4.0 17.4 + - - +
87A PHE 3.5 0.2 - - - -
88A ILE* 1.3 77.4 - - - +
90A LYS* 1.3 57.6 + - + +
92A LEU 3.3 0.6 + - - +
93A LYS 3.0 8.5 + - - -
94A LEU* 2.7 54.4 + - + +
95A VAL 3.5 15.7 - - - +
96A ALA* 3.1 21.7 + - - +
98A GLU 2.6 27.7 + - - +
99A GLN* 4.6 2.2 - - - +
100A LEU* 3.9 21.1 - - + +
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Residues in contact with LYS 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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86A ASP* 3.1 33.3 + - - +
87A PHE* 4.0 8.4 - - - +
88A ILE 3.2 1.0 - - - -
89A LYS* 1.3 77.2 - - + +
91A PHE* 1.3 63.0 + - + +
93A LYS* 3.6 11.6 + - - +
94A LEU 5.0 2.7 - - - +
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Residues in contact with PHE 91 (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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68A MET* 3.5 29.8 - - + -
69A LYS* 5.8 9.6 - - + -
70A THR* 5.7 5.2 - - - -
73A TRP* 3.9 21.8 - + - -
87A PHE* 3.5 45.5 - + - -
88A ILE 2.9 8.7 + - - +
90A LYS* 1.3 79.3 - - + +
92A LEU* 1.3 61.8 + - + +
93A LYS* 3.1 16.0 + - - +
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Residues in contact with LEU 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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65A THR* 4.8 0.9 - - - +
66A PRO* 3.3 59.4 - - + +
67A ILE 3.9 11.2 - - - +
68A MET* 3.8 21.5 - - + -
88A ILE* 3.0 36.1 + - + +
89A LYS 4.1 0.2 - - - +
91A PHE* 1.3 77.6 - - + +
93A LYS* 1.3 72.8 + - - +
94A LEU* 3.2 32.2 + - + +
100A LEU* 4.5 4.0 - - + -
133A TYR* 3.7 16.4 - - + -
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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