Contacts of the helix formed by residues 84 - 97 (chain B) in PDB entry 1GKU
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 LYS 84 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B TRP* 4.3 17.0 - - + -
76B ALA* 5.4 5.8 + - + -
77B THR* 5.6 1.4 - - - +
78B ALA* 4.6 29.2 + - - +
79B PRO 5.9 0.2 - - - -
80B THR* 6.4 1.3 - - - +
82B VAL 3.4 14.6 + - - +
83B GLY* 1.3 73.2 - - - +
85B THR* 1.3 63.5 + - - +
86B SER* 3.2 1.1 + - - -
87B PHE* 3.0 7.4 + - - +
88B GLY 2.9 24.6 + - - -
180B PHE* 3.5 12.9 - - + -
182B ASP* 5.5 2.7 - - - +
221B MET* 5.3 2.5 - - + -
223B SER* 4.0 38.0 + - - +
224B THR* 6.0 1.0 - - - +
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Residues in contact with THR 85 (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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84B LYS* 1.3 78.4 - - - +
86B SER* 1.3 64.3 + - - +
89B LEU* 2.9 47.5 + - + +
106B PHE* 4.3 19.6 - - + -
180B PHE* 3.9 12.7 - - + -
182B ASP* 3.2 26.0 + - - -
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Residues in contact with SER 86 (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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50B PHE* 4.8 2.7 - - - -
54B VAL* 4.2 15.9 - - - +
61B GLN* 4.7 2.3 + - - -
83B GLY* 3.6 22.2 + - - -
84B LYS 4.2 0.4 - - - +
85B THR* 1.3 79.5 - - - +
87B PHE* 1.3 64.3 + - - +
89B LEU* 3.9 3.5 + - - -
90B ALA* 3.3 19.8 + - - +
118B THR* 6.1 0.2 - - - -
122B TYR* 3.4 27.3 + - - -
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Residues in contact with PHE 87 (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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46B PHE* 3.9 23.3 - + - -
50B PHE* 4.1 19.7 - + + -
57B PRO* 6.2 0.4 - - + -
61B GLN* 3.6 36.6 - - + +
64B TRP* 3.8 35.4 - + + -
65B ALA 4.0 7.0 - - - -
68B ILE* 3.9 14.8 - - + -
83B GLY 3.8 14.1 - - - +
84B LYS 3.0 7.9 + - - +
86B SER* 1.3 79.4 + - - +
88B GLY* 1.3 68.1 + - - +
90B ALA* 3.0 2.8 + - - +
91B MET* 2.9 32.4 + - + +
178B PHE* 5.7 0.2 - + - -
221B MET* 3.7 31.2 - - + -
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Residues in contact with GLY 88 (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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84B LYS 2.9 14.6 + - - -
85B THR 3.2 1.3 + - - -
87B PHE* 1.3 76.8 - - - +
89B LEU* 1.3 57.6 + - - +
91B MET* 3.2 4.6 + - - +
92B SER* 2.8 33.1 + - - -
104B VAL* 5.6 1.3 - - - -
178B PHE* 4.1 5.6 - - - -
180B PHE* 3.5 35.7 - - - -
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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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85B THR* 2.9 39.7 + - + +
86B SER* 4.0 2.9 - - - +
88B GLY* 1.3 75.0 - - - +
90B ALA* 1.3 61.4 + - - +
92B SER* 3.8 4.3 - - - -
93B LEU* 3.2 22.3 + - - +
104B VAL* 4.1 26.9 - - + -
106B PHE* 4.6 0.9 - - + -
115B ALA* 4.2 20.9 - - + +
118B THR* 4.1 27.6 - - + +
119B ILE* 3.5 32.8 - - + +
122B TYR* 3.9 15.3 - - + -
160B ILE* 5.0 0.2 - - + -
180B PHE* 5.7 0.6 - - + -
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Residues in contact with ALA 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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46B PHE* 4.0 2.5 - - + -
49B PHE* 3.1 21.7 - - + -
50B PHE* 3.6 31.6 - - + -
53B CYS* 4.9 2.2 - - - -
54B VAL* 4.3 8.3 - - + -
86B SER 3.3 15.7 + - - +
87B PHE 3.0 4.7 + - - +
89B LEU* 1.3 76.8 - - - +
91B MET* 1.3 61.1 + - - +
93B LEU* 3.6 1.0 + - - +
94B PHE* 3.1 22.5 + - - +
122B TYR* 4.1 10.3 - - + -
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Residues in contact with MET 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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46B PHE* 3.5 39.4 - - + -
65B ALA* 4.0 32.3 - - + +
68B ILE* 4.3 19.7 - - + -
69B LEU* 4.5 7.6 - - + -
87B PHE* 2.9 24.8 + - + +
88B GLY* 3.7 4.7 - - - +
90B ALA* 1.3 72.9 - - - +
92B SER* 1.3 58.4 + - - +
94B PHE* 3.3 3.4 + - - +
95B LEU* 2.7 70.4 + - + +
178B PHE* 4.0 14.1 - - + -
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Residues in contact with SER 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B GLY 2.8 18.0 + - - -
89B LEU* 3.8 6.5 - - - -
91B MET* 1.3 77.5 - - - +
93B LEU* 1.3 62.7 + - - +
95B LEU 3.3 0.2 + - - -
96B ALA* 2.9 24.9 + - - +
102B CYS* 3.1 35.3 - - - +
104B VAL* 3.8 16.5 - - - +
119B ILE* 5.0 1.6 - - - -
158B ILE* 3.7 21.3 - - - +
178B PHE* 4.2 5.6 - - - -
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Residues in contact with LEU 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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49B PHE* 3.4 24.0 - - + -
89B LEU 3.2 15.7 + - - +
90B ALA 3.7 3.4 - - - +
91B MET 3.2 0.2 - - - -
92B SER* 1.3 77.5 - - - +
94B PHE* 1.3 56.2 + - - +
96B ALA* 2.7 24.3 + - - +
97B LEU* 2.9 28.3 + - + +
119B ILE* 4.2 18.2 - - + +
122B TYR* 3.7 30.3 - - + -
123B ALA* 3.9 13.2 - - - +
127B GLY 5.6 0.2 - - - +
128B VAL* 3.9 26.2 - - + -
133B LEU* 5.0 2.2 - - + -
158B ILE* 3.7 16.5 - - + +
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Residues in contact with PHE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.7 25.8 - - + -
45B GLU* 4.1 11.4 - - + -
46B PHE* 3.5 35.9 - + + -
49B PHE* 3.4 37.0 - + + -
69B LEU* 4.4 10.8 - - + -
90B ALA 3.1 16.3 + - - +
91B MET* 3.5 4.5 - - - +
93B LEU* 1.3 79.8 - - - +
95B LEU* 1.3 83.9 + - + +
97B LEU* 3.5 11.2 + - + +
98B LYS* 3.4 53.6 - - + +
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Residues in contact with LEU 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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42B LEU* 6.4 0.2 - - + -
68B ILE* 4.3 8.5 - - + -
69B LEU* 4.4 12.3 - - + -
91B MET* 2.7 43.8 + - + +
94B PHE* 1.3 95.7 - - + +
96B ALA* 1.3 60.0 + - - +
98B LYS* 3.1 11.8 + - + +
100B LYS* 2.9 51.1 + - + +
102B CYS* 3.5 11.0 - - - -
177B ASP* 5.8 0.7 - - + -
178B PHE* 3.8 32.8 - - + -
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Residues in contact with ALA 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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92B SER 2.9 5.8 + - - +
93B LEU 2.7 15.4 + - - +
95B LEU* 1.3 67.6 - - - +
97B LEU* 1.3 54.5 + - + +
98B LYS 2.9 4.7 - - - -
99B GLY* 2.7 22.7 + - - -
100B LYS 4.0 7.0 - - - +
101B ARG 4.6 2.7 - - - +
102B CYS* 4.3 0.9 - - - -
133B LEU* 4.0 11.8 - - + +
157B LYS* 3.7 27.1 + - + +
158B ILE* 3.3 35.9 - - + -
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Residues in contact with LEU 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49B PHE* 3.9 28.9 - - + -
93B LEU* 2.9 32.1 + - + +
94B PHE* 3.8 9.6 - - + +
96B ALA* 1.3 76.1 - - - +
98B LYS* 1.3 67.5 + - + +
99B GLY 3.3 1.1 + - - -
126B ALA* 5.8 5.6 - - + -
127B GLY 4.1 20.9 - - - +
128B VAL* 4.5 11.9 - - + -
129B GLY 5.0 2.0 - - - +
133B LEU* 4.8 10.8 - - + -
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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