Contacts of the helix formed by residues 78 - 90 (chain A) in PDB entry 4WUR
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 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ASP* 2.7 16.5 + - - +
77A PRO* 1.3 82.5 - - + +
79A PHE* 1.3 66.4 + - - +
80A LEU 3.3 2.2 - - - -
81A HIS* 3.3 12.3 + - - +
82A ARG* 2.6 54.6 + - - +
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Residues in contact with PHE 79 (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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72A TYR* 3.6 29.4 - + - -
75A VAL* 3.5 30.3 - - + -
76A ASP* 2.9 18.2 + - - +
77A PRO 3.2 0.2 - - - -
78A THR* 1.3 78.4 + - - +
80A LEU* 1.3 64.2 + - + +
82A ARG* 3.0 24.8 + - - +
83A PHE* 2.7 42.0 + + + +
151A LEU* 3.6 25.1 - - + -
154A ALA* 3.6 26.0 - - + -
155A TYR* 3.7 34.3 - + - -
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Residues in contact with LEU 80 (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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10A VAL* 4.6 7.0 - - + -
56A LEU 3.7 20.6 - - - +
57A ALA* 3.6 26.9 - - - +
60A LEU* 4.2 14.4 - - + -
68A LEU* 3.6 36.3 - - + -
72A TYR* 4.7 8.5 - - + -
75A VAL* 5.4 0.4 - - - +
76A ASP 4.7 0.2 + - - -
77A PRO 4.4 2.1 + - - +
78A THR 3.3 0.4 - - - -
79A PHE* 1.3 82.3 - - + +
81A HIS* 1.3 64.1 + - - +
83A PHE* 3.7 10.1 - - + +
84A TYR* 2.9 65.6 + - + +
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Residues in contact with HIS 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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27A ARG* 6.3 0.4 - - - -
32A CYS* 3.4 21.0 - - - -
34A PHE* 4.1 9.6 - + - -
39A ASP* 3.4 22.4 + - - -
57A ALA* 3.8 16.5 + - + +
77A PRO 5.6 0.4 - - - +
78A THR* 3.3 14.8 + - - +
80A LEU* 1.3 78.3 - - - +
82A ARG* 1.3 65.4 + - + +
84A TYR* 3.9 1.4 - - - +
85A SER* 2.9 43.0 + - - -
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Residues in contact with ARG 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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76A ASP* 2.5 28.9 + - - -
78A THR* 2.6 33.6 + - - +
79A PHE* 3.5 19.4 - - - +
81A HIS* 1.3 82.9 - - + +
83A PHE* 1.3 59.7 + - - +
85A SER* 3.3 6.4 + - - -
86A LEU* 2.9 42.3 + - + +
154A ALA* 2.9 33.3 + - + +
157A ASN* 3.6 37.4 + - - +
158A CYS 5.2 4.9 + - - +
159A THR* 6.3 2.7 - - - -
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Residues in contact with PHE 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A TYR* 3.5 35.2 - + - -
79A PHE* 2.7 26.2 + + + +
80A LEU* 3.7 5.8 - - + +
82A ARG* 1.3 75.2 - - - +
84A TYR* 1.3 74.7 + + - +
86A LEU* 3.7 2.5 - - - +
87A LYS* 2.9 52.4 + - + +
147A ASP* 4.0 10.8 - - + -
150A ALA* 3.9 4.5 - - + -
151A LEU* 3.3 56.3 - - + -
154A ALA* 3.9 14.3 - - + +
402A IPA 5.2 1.3 - - - -
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Residues in contact with TYR 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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10A VAL* 3.9 14.7 + - - -
34A PHE* 3.5 46.6 - + + -
37A GLY* 4.7 0.3 - - - +
55A TYR* 3.4 36.2 - + + +
56A LEU 3.6 26.1 + - - -
57A ALA* 4.3 4.5 - - + -
72A TYR* 4.8 4.0 - - - -
80A LEU* 2.9 42.9 + - + +
83A PHE* 1.3 91.8 - + - +
85A SER* 1.3 64.0 + - - +
87A LYS* 3.3 9.2 - - + +
88A ALA* 3.2 17.7 + - - +
402A IPA 3.7 31.0 - - + +
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Residues in contact with SER 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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34A PHE* 3.8 17.0 - - - -
39A ASP* 5.8 0.4 - - - -
81A HIS* 2.9 33.2 + - - -
82A ARG* 3.3 10.0 + - - -
84A TYR* 1.3 73.4 - - - +
86A LEU* 1.3 69.5 + - - +
88A ALA* 3.0 7.1 + - - +
89A ALA* 2.9 23.8 + - - +
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Residues in contact with LEU 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* 2.9 29.2 + - + +
83A PHE 3.7 3.1 - - - +
85A SER* 1.3 77.7 + - - +
87A LYS* 1.3 63.3 - - - +
89A ALA* 3.7 5.2 - - - +
90A VAL* 2.9 28.9 + - - +
150A ALA* 3.5 17.0 - - + +
153A MET* 3.6 28.5 - - + -
154A ALA* 3.3 37.7 - - + +
158A CYS 4.2 10.3 - - - +
159A THR* 4.8 0.2 - - - -
160A PHE* 3.9 32.8 - - + +
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Residues in contact with LYS 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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83A PHE* 2.9 39.7 + - + +
84A TYR* 3.3 11.7 - - - +
85A SER 3.1 0.2 - - - -
86A LEU* 1.3 77.9 - - - +
88A ALA* 1.3 62.6 + - - +
90A VAL* 3.4 2.0 + - - -
91A HIS* 3.2 19.8 + - - +
139A LYS* 5.6 0.4 - - - +
146A THR* 4.0 16.7 - - + +
147A ASP* 2.6 32.5 + - - +
150A ALA* 3.6 22.1 - - + +
402A IPA 3.3 44.0 + - + +
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Residues in contact with ALA 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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34A PHE* 5.4 0.9 - - + -
37A GLY* 3.2 29.8 - - - +
84A TYR 3.2 6.0 + - - +
85A SER* 3.0 10.7 + - - +
87A LYS* 1.3 78.0 - - - +
89A ALA* 1.3 64.1 + - - +
91A HIS* 3.3 19.0 + - - +
92A GLY 4.8 0.3 + - - -
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Residues in contact with ALA 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 SER 2.9 16.0 + - - +
86A LEU* 3.7 4.9 - - - +
88A ALA* 1.3 78.9 - - - +
90A VAL* 1.3 60.7 + - - +
91A HIS 3.5 0.5 + - - -
92A GLY* 4.4 4.5 + - - -
93A TRP* 4.6 2.1 + - - -
160A PHE* 3.3 52.3 - - + -
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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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86A LEU 2.9 15.0 + - - +
88A ALA 3.2 0.2 - - - -
89A ALA* 1.3 76.3 - - - +
91A HIS* 1.3 62.3 + - - +
92A GLY 3.1 4.2 + - - -
93A TRP* 3.2 65.3 + - + +
146A THR* 4.0 22.9 - - + +
149A ILE* 4.1 18.4 - - + -
150A ALA* 4.8 1.3 - - + +
153A MET* 3.5 15.5 - - + -
160A PHE* 3.8 7.9 - - + -
401A IPA 3.9 9.1 - - + +
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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