Contacts of the helix formed by residues 83 - 99 (chain A) in PDB entry 5WF3
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 83 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82A ARG* 1.3 77.4 - - - +
84A ARG* 1.3 64.4 + - - +
85A ILE* 3.2 30.6 + - + +
86A MET* 2.9 31.6 + - - +
87A ALA* 3.0 18.9 + - - +
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Residues in contact with ARG 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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23A GLU* 6.2 3.4 - - + +
24A TYR* 4.7 19.5 - - + +
82A ARG 3.7 1.3 + - - -
83A ASP* 1.3 73.3 - - - +
85A ILE* 1.3 71.5 + - + +
87A ALA* 3.7 4.4 - - - +
88A TRP* 3.1 37.3 + - + +
106A LEU* 4.5 8.7 - - + +
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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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83A ASP* 3.2 14.8 + - + +
84A ARG* 1.3 85.0 - - + +
86A MET* 1.3 58.6 + - + +
88A TRP* 3.4 7.2 + - - +
89A THR* 2.7 40.1 + - - +
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Residues in contact with MET 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 ARG* 4.4 22.7 - - + +
83A ASP* 2.9 24.7 + - - +
85A ILE* 1.3 77.5 - - + +
87A ALA* 1.3 65.6 + - - +
89A THR* 3.0 22.3 + - + +
90A VAL* 2.9 34.5 + - + +
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Residues in contact with ALA 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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79A ILE* 3.8 33.2 - - + +
82A ARG* 4.0 14.4 - - + +
83A ASP 3.0 19.2 + - - +
84A ARG 3.7 4.0 - - - +
86A MET* 1.3 77.4 - - - +
88A TRP* 1.3 63.6 + - - +
90A VAL* 3.2 3.0 + - - +
91A VAL* 3.0 25.3 + - - +
106A LEU* 3.8 20.0 - - + -
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Residues in contact with TRP 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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84A ARG* 3.1 30.3 + - + +
85A ILE* 3.8 6.3 - - - +
87A ALA* 1.3 79.3 - - - +
89A THR* 1.3 55.7 + - - +
91A VAL* 3.7 26.0 - - + +
92A ASN* 2.6 43.5 + - - +
102A LYS* 4.2 20.6 - - - -
103A PRO* 3.4 27.1 - - + -
104A LYS 3.8 15.9 - - - -
105A PHE* 3.9 10.1 - - - -
106A LEU* 3.6 37.1 - - + +
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Residues in contact with THR 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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85A ILE* 2.7 27.9 + - - +
86A MET* 3.0 30.8 + - + +
88A TRP* 1.3 76.3 - - - +
90A VAL* 1.3 58.3 + - + +
92A ASN* 3.3 8.9 + - - +
93A SER* 3.0 36.3 + - - +
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Residues in contact with VAL 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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77A GLU* 3.7 35.4 - - + +
79A ILE* 4.9 7.0 - - + -
82A ARG* 4.2 28.9 - - - +
86A MET* 2.9 29.4 + - + +
87A ALA* 3.8 4.3 - - - +
89A THR* 1.3 72.2 - - + +
91A VAL* 1.3 60.6 + - - +
93A SER* 3.1 8.4 + - - -
94A ILE* 2.8 36.6 + - + +
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Residues in contact with VAL 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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79A ILE* 4.1 13.9 - - + -
87A ALA 3.0 21.3 + - - +
88A TRP* 3.7 24.0 - - + +
89A THR 3.3 0.2 - - - -
90A VAL* 1.3 76.3 - - - +
92A ASN* 1.3 58.6 + - - +
94A ILE* 3.2 7.7 + - - +
95A CYS* 2.8 35.3 + - - -
102A LYS* 4.6 4.0 - - + -
103A PRO* 4.0 25.4 - - + -
106A LEU* 4.3 5.4 - - + -
107A PRO* 4.1 19.5 - - + -
117A PHE* 4.0 18.2 - - + -
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Residues in contact with ASN 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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88A TRP* 2.6 38.0 + - - +
89A THR* 3.6 6.9 - - - +
90A VAL 3.3 0.2 - - - -
91A VAL* 1.3 75.3 - - - +
93A SER* 1.3 58.5 + - - +
95A CYS* 4.5 2.5 - - - +
96A ASN* 2.3 48.7 + - - +
102A LYS* 2.8 42.8 + - - +
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Residues in contact with SER 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 THR* 3.0 21.0 + - - +
90A VAL* 3.5 11.8 - - - -
92A ASN* 1.3 77.5 - - - +
94A ILE* 1.3 54.0 + - - +
96A ASN* 3.5 3.6 + - - -
97A THR* 2.5 42.2 + - - +
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Residues in contact with ILE 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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77A GLU* 3.9 12.3 - - + -
79A ILE* 4.4 4.0 - - + -
90A VAL* 2.8 42.1 + - + +
91A VAL 3.6 4.3 - - - +
93A SER* 1.3 71.6 - - - +
95A CYS* 1.3 57.1 + - - +
97A THR* 3.0 6.6 + - - -
98A THR* 2.8 36.0 + - + +
110A TYR* 3.6 52.0 - - + -
112A TYR* 3.9 18.6 - - + +
117A PHE* 3.5 29.2 - - + -
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Residues in contact with CYS 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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91A VAL* 2.8 29.7 + - - +
92A ASN* 3.9 4.5 - - - +
94A ILE* 1.3 77.9 - - - +
96A ASN* 1.3 63.0 + - - +
97A THR 3.0 0.7 + - - -
98A THR* 4.4 2.2 - - - -
99A GLY* 2.8 32.6 + - - -
100A VAL* 3.5 23.7 - - - +
101A GLU 3.8 4.5 - - - -
102A LYS* 3.7 32.1 - - + -
117A PHE* 3.8 17.3 - - - -
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Residues in contact with ASN 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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92A ASN* 2.3 54.9 + - - +
93A SER* 3.8 3.8 - - - +
95A CYS* 1.3 75.7 - - - +
97A THR* 1.3 61.9 + - + +
99A GLY 4.8 0.7 - - - -
102A LYS* 6.2 0.2 - - - +
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Residues in contact with THR 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 SER* 2.5 26.0 + - - +
94A ILE* 3.0 13.7 + - - -
95A CYS 3.0 0.2 - - - -
96A ASN* 1.3 82.3 - - + +
98A THR* 1.3 65.6 + - - +
99A GLY 3.7 0.7 - - - -
112A TYR* 6.0 1.0 - - - -
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Residues in contact with THR 98 (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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94A ILE* 2.8 21.9 + - + +
97A THR* 1.3 85.0 - - - +
99A GLY* 1.3 58.1 + - - +
100A VAL* 3.0 24.2 + - - +
110A TYR* 3.3 35.0 + - + +
112A TYR* 4.9 9.4 - - + -
115A ASN* 5.0 7.6 - - - +
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Residues in contact with GLY 99 (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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95A CYS 2.8 13.0 + - - -
96A ASN 4.8 0.8 - - - -
97A THR 3.7 1.4 - - - -
98A THR* 1.3 74.7 - - - +
100A VAL* 1.3 66.7 + - - +
101A GLU 3.5 1.2 + - - -
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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