Contacts of the helix formed by residues 78 - 95 (chain F) in PDB entry 2WA9
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 ALA 78 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F SER* 3.2 16.6 + - - +
28F TYR* 3.8 29.1 - - + -
76F PHE 4.0 0.2 + - - -
77F THR* 1.3 72.2 - - - +
79F GLU* 1.3 65.4 + - + +
81F ALA* 3.2 2.9 + - - +
82F GLU* 3.0 33.7 + - - +
103F LEU* 5.3 0.3 - - - +
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Residues in contact with GLU 79 (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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77F THR* 3.3 3.9 + - - +
78F ALA* 1.3 79.7 - - + +
80F VAL* 1.3 65.2 + - + +
82F GLU* 3.4 14.0 + - - +
83F THR* 3.1 26.9 + - - -
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Residues in contact with VAL 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F PHE* 3.9 28.5 - - + -
77F THR* 3.2 23.3 + - - +
79F GLU* 1.3 76.6 - - + +
81F ALA* 1.3 62.5 + - - +
83F THR* 3.5 7.8 + - - -
84F LYS* 3.1 39.1 + - - +
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Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28F TYR* 3.8 13.9 - - + -
30F VAL* 3.7 19.6 - - + +
76F PHE* 4.0 6.9 - - + +
77F THR 2.9 16.9 + - - +
78F ALA 3.5 4.3 - - - +
80F VAL* 1.3 74.9 - - - +
82F GLU* 1.3 59.0 + - - +
84F LYS* 3.2 3.7 + - - +
85F VAL* 2.9 33.6 + - - +
103F LEU* 3.5 24.2 - - + -
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Residues in contact with GLU 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78F ALA* 3.0 21.9 + - - +
79F GLU* 3.6 15.0 - - - +
81F ALA* 1.3 72.7 - - - +
83F THR* 1.3 66.0 + - - +
84F LYS 3.2 0.3 + - - -
85F VAL* 3.4 4.9 + - - +
86F ALA* 3.1 27.9 + - - +
103F LEU* 4.1 20.3 - - + +
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Residues in contact with THR 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79F GLU 3.1 12.5 + - - -
80F VAL* 3.5 11.8 - - - +
82F GLU* 1.3 78.5 - - - +
84F LYS* 1.3 56.7 + - + +
86F ALA* 3.9 3.7 - - - +
87F MET* 3.0 51.0 + - + +
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Residues in contact with LYS 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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30F VAL* 4.6 13.7 - - + -
50F PHE* 2.4 37.3 + - + +
51F PHE* 4.7 7.0 - - + +
76F PHE* 4.4 29.6 - - + -
80F VAL* 3.1 30.4 + - + +
81F ALA* 3.5 10.3 - - - +
82F GLU 3.2 0.4 - - - -
83F THR* 1.3 73.0 - - - +
85F VAL* 1.3 58.2 + - - +
87F MET* 2.9 25.0 + - + +
88F VAL* 2.7 42.1 + - + +
101F CYS* 5.2 0.2 - - - -
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Residues in contact with VAL 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30F VAL* 4.6 5.4 - - + -
81F ALA 2.9 20.5 + - - +
82F GLU* 3.8 4.5 - - - +
84F LYS* 1.3 77.1 - - - +
86F ALA* 1.3 57.9 + - - +
88F VAL* 3.1 1.9 + - - +
89F ASN* 2.8 49.9 + - - +
101F CYS* 3.2 23.6 - - - +
102F THR* 3.6 26.2 - - - +
103F LEU* 3.7 22.7 - - + -
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Residues in contact with ALA 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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82F GLU 3.1 14.4 + - - +
83F THR* 4.1 4.0 - - - +
85F VAL* 1.3 81.8 - - - +
87F MET* 1.3 56.3 + - - +
89F ASN* 3.9 6.5 - - - +
90F LYS* 3.0 28.4 + - - +
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Residues in contact with MET 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50F PHE* 3.5 33.3 - - + -
83F THR* 3.0 34.5 + - + +
84F LYS* 2.9 42.6 + - + +
86F ALA* 1.3 73.8 - - - +
88F VAL* 1.3 62.0 + - - +
90F LYS* 3.2 6.4 + - - +
91F TYR* 3.0 30.1 + - - +
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Residues in contact with VAL 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32F LEU* 4.2 4.9 - - + -
46F VAL* 4.1 24.5 - - + +
50F PHE* 4.1 26.2 - - + -
51F PHE* 4.1 20.6 - - + -
84F LYS* 2.7 26.5 + - - +
85F VAL 3.6 3.6 - - - +
87F MET* 1.3 74.4 - - - +
89F ASN* 1.3 61.4 + - - +
91F TYR* 3.6 6.2 + - - +
92F ALA* 3.1 24.0 + - + +
99F LEU* 4.8 7.4 - - + +
101F CYS* 3.6 30.5 - - + -
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Residues in contact with ASN 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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85F VAL* 2.8 36.5 + - - +
86F ALA* 4.1 6.2 - - - +
88F VAL* 1.3 75.8 - - - +
90F LYS* 1.3 63.1 + - - +
92F ALA* 3.4 4.8 + - - +
93F ARG* 3.1 36.1 + - + +
99F LEU 3.6 10.3 - - - +
100F LEU* 3.7 12.9 - - - +
101F CYS* 3.1 41.6 + - - +
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Residues in contact with LYS 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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86F ALA 3.0 19.1 + - - +
87F MET* 3.2 7.6 + - - +
89F ASN* 1.3 76.0 - - - +
91F TYR* 1.3 62.9 + - - +
93F ARG* 3.2 7.1 + - - +
94F GLU* 3.1 45.3 + - - +
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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
----------------------------------------------------------
42F PHE* 3.5 25.6 - + - -
45F ASP* 2.5 37.4 + - - -
46F VAL* 4.3 7.4 - - + -
49F LYS* 3.7 27.2 - - + -
50F PHE* 3.5 32.5 - + + -
87F MET 3.0 15.8 + - - +
88F VAL 3.8 4.3 - - - +
90F LYS* 1.3 77.2 - - - +
92F ALA* 1.3 60.9 + - - +
94F GLU* 3.3 22.9 - - - +
95F ASN* 3.2 43.1 + - - +
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Residues in contact with ALA 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F PHE* 3.6 25.8 - - + -
88F VAL 3.1 18.3 + - - +
89F ASN 3.7 2.2 - - - +
91F TYR* 1.3 74.9 - - - +
93F ARG* 1.3 79.0 + - - +
95F ASN 3.3 2.1 + - - -
96F GLU 3.0 7.4 + - - -
97F HIS* 2.8 32.1 + - - +
99F LEU* 4.0 15.9 - - + +
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Residues in contact with ARG 93 (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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89F ASN* 3.1 27.4 + - + +
90F LYS* 3.2 5.6 + - - +
92F ALA* 1.3 100.7 - - - +
94F GLU* 1.3 57.1 + - - +
96F GLU* 3.0 21.4 + - - +
97F HIS 2.7 30.1 + - - +
98F PRO* 3.3 23.4 + - - +
99F LEU 3.3 13.7 + - - -
100F LEU* 3.9 17.6 - - - +
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Residues in contact with GLU 94 (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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90F LYS* 3.1 34.3 + - - +
91F TYR* 3.3 38.4 + - - +
93F ARG* 1.3 77.6 - - - +
95F ASN* 1.3 68.8 + - - +
96F GLU* 3.2 9.6 + - - +
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Residues in contact with ASN 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F PHE* 3.8 25.6 - - + -
45F ASP* 5.4 0.5 - - - +
91F TYR* 3.2 38.1 + - - +
92F ALA 3.3 0.6 + - - +
93F ARG 3.2 0.2 - - - -
94F GLU* 1.3 89.2 + - - +
96F GLU* 1.3 69.4 + - - +
97F HIS* 3.2 23.2 + - + +
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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