Contacts of the helix formed by residues 78 - 91 (chain F) in PDB entry 2PGW
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 ASP 78 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126C HIS* 5.5 0.3 - - - -
127C GLN* 3.2 23.7 - - - +
130C GLY 3.4 5.4 - - - -
131C GLY* 3.8 11.1 - - - -
132C ALA* 4.3 4.4 + - - -
74F HIS* 5.8 0.8 - - + +
75F SER* 3.1 26.2 + - - +
77F HIS* 1.3 81.3 - - - +
79F VAL* 1.3 63.6 + - - +
80F ALA 3.3 2.2 - - - -
81F PRO* 3.1 11.8 - - + +
82F LEU* 3.0 35.4 + - + +
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Residues in contact with VAL 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130C GLY* 3.4 8.9 + - - +
76F PRO 3.7 2.7 + - - +
77F HIS 3.3 0.4 - - - -
78F ASP* 1.3 75.8 - - - +
80F ALA* 1.3 70.2 + - - +
82F LEU* 3.6 2.3 - - - +
83F ILE* 3.0 36.8 + - + +
110F ASP* 3.5 21.8 - - - +
113F MSE 3.6 45.9 - - + +
114F TRP* 3.9 21.8 - - + +
117F GLN* 3.7 20.9 - - - +
279F GLN* 4.2 2.5 - - - +
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Residues in contact with ALA 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C LEU 5.2 0.4 - - - +
130C GLY* 2.9 25.4 + - - +
133C HIS* 3.6 22.2 - - + +
79F VAL* 1.3 75.1 - - - +
81F PRO* 1.3 65.0 - - + +
83F ILE* 3.4 5.2 + - - +
84F ALA* 3.1 22.5 + - - +
279F GLN* 3.3 23.8 - - - +
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Residues in contact with PRO 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130C GLY 3.1 14.8 - - - +
131C GLY 3.9 8.7 - - - +
132C ALA 3.3 27.1 - - - +
133C HIS* 3.6 22.2 - - + +
78F ASP* 3.1 28.9 - - + +
80F ALA* 1.3 85.4 - - + +
82F LEU* 1.3 55.6 + - + +
84F ALA* 3.4 4.7 + - + +
85F ARG* 2.9 30.5 + - - +
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Residues in contact with LEU 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F HIS 5.0 2.0 - - - +
71F LEU* 4.1 19.7 - - + +
74F HIS* 3.9 43.5 - - + +
75F SER 3.6 22.4 - - - +
78F ASP* 3.0 34.6 + - + +
79F VAL* 3.6 4.3 - - - +
81F PRO* 1.3 77.6 - - + +
83F ILE* 1.3 57.4 + - + +
85F ARG* 3.2 16.2 + - - +
86F ILE* 2.9 36.8 + - + +
113F MSE 3.7 13.7 - - + -
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Residues in contact with ILE 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71F LEU* 5.8 1.1 - - + -
79F VAL* 3.0 38.7 + - + +
80F ALA* 3.9 4.0 - - - +
82F LEU* 1.3 76.7 - - + +
84F ALA* 1.3 59.1 + - - +
86F ILE* 3.3 4.4 + - + +
87F PHE* 2.8 29.9 + - + +
106F PHE* 3.5 50.2 - - + -
109F ILE* 4.4 9.2 - - + -
110F ASP* 4.0 28.9 - - + +
276F GLY 5.1 2.5 - - - +
280F PRO* 6.5 0.4 - - + -
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Residues in contact with ALA 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C HIS* 5.0 8.5 - - + +
318C PRO* 6.4 0.7 - - + -
80F ALA 3.1 17.9 + - - +
81F PRO* 3.6 7.9 - - + +
83F ILE* 1.3 78.5 - - - +
85F ARG* 1.3 57.3 + - - +
87F PHE* 3.5 9.3 + - - +
88F HIS* 3.0 28.6 + - - +
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Residues in contact with ARG 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B TYR* 3.5 28.2 + - + +
70F HIS* 3.6 41.8 + - - +
74F HIS* 4.7 10.6 + - - -
81F PRO 2.9 17.9 + - - +
82F LEU* 3.6 15.8 + - - +
83F ILE 3.2 0.2 - - - -
84F ALA* 1.3 75.0 - - - +
86F ILE* 1.3 68.7 + - - +
88F HIS* 3.2 1.7 + - - -
89F GLN* 2.5 60.1 + - - +
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Residues in contact with ILE 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67F LEU* 3.6 48.7 - - + +
70F HIS* 3.7 34.5 - - + -
71F LEU* 3.9 21.8 - - + -
82F LEU* 2.9 26.0 + - + +
83F ILE* 3.7 8.5 - - + +
85F ARG* 1.3 84.2 - - - +
87F PHE* 1.3 58.6 + - - +
89F GLN* 4.7 4.3 - - - -
90F GLU* 2.9 34.3 + - + +
106F PHE* 3.9 10.3 - - + -
109F ILE* 5.6 1.8 - - + -
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Residues in contact with PHE 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B TRP* 3.8 28.9 - + - -
83F ILE* 2.8 19.3 + - + +
84F ALA* 3.6 9.4 - - - +
86F ILE* 1.3 76.7 - - - +
88F HIS* 1.3 57.5 + - - +
91F TYR* 3.0 61.1 + + + +
92F LEU* 3.2 29.8 + - + -
98F ILE 4.4 2.5 - - - -
99F MSE 3.9 30.1 - - + -
102F ALA* 3.5 26.5 - - + -
106F PHE* 3.7 14.1 - + + -
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Residues in contact with HIS 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B SER* 3.4 35.7 + - - -
26B TYR* 2.9 24.4 + + - +
84F ALA 3.0 16.6 + - - +
85F ARG* 3.6 0.9 - - - +
87F PHE* 1.3 78.4 - - + +
89F GLN* 1.3 56.5 + - - +
92F LEU* 3.7 31.2 - - + -
93F GLY* 2.7 36.4 + - - -
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Residues in contact with GLN 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B TRP* 3.3 21.9 - - + -
26B TYR* 3.5 41.9 - - + +
70F HIS* 4.0 23.2 - - - -
85F ARG* 2.5 50.8 + - - +
86F ILE* 4.0 2.9 - - - +
88F HIS* 1.3 78.5 - - - +
90F GLU* 1.3 64.5 + - + +
94F HIS* 3.2 22.0 + - - -
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Residues in contact with GLU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ALA* 3.8 1.6 - - - +
55B PRO* 3.6 29.0 - - + +
66F ARG* 3.0 48.0 + - - +
67F LEU* 4.5 7.9 - - + -
70F HIS* 2.8 35.4 + - + +
86F ILE* 2.9 28.2 + - + +
89F GLN* 1.3 82.6 + - + +
91F TYR* 1.3 68.6 + - + +
94F HIS* 3.3 20.4 + - - -
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Residues in contact with TYR 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B PRO* 3.7 35.6 - - + +
63F ILE* 3.8 7.6 - - - +
67F LEU* 3.7 31.8 - - + +
87F PHE* 3.0 40.3 + + + +
89F GLN 3.5 0.4 - - - -
90F GLU* 1.3 82.1 - - + +
92F LEU* 1.3 66.8 + - - +
93F GLY 3.3 1.3 - - - -
94F HIS* 3.0 13.3 + - - +
96F ALA* 3.1 32.9 + - + +
98F ILE* 3.6 35.2 - - + -
101F ALA* 4.5 1.8 + - + -
102F ALA* 3.6 33.0 - - + -
105F ILE* 4.0 5.5 - - - +
106F PHE* 4.2 3.4 - + - -
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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