Contacts of the helix formed by residues 84 - 94 (chain A) in PDB entry 5X6G
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 LEU 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A ASP 5.2 2.2 - - - +
74A GLY 4.4 7.2 - - - +
75A ARG* 4.6 13.9 - - + -
83A GLY* 1.4 73.8 - - - -
85A PRO* 1.3 72.8 - - + +
86A HIS* 3.8 13.2 - - + -
87A VAL* 3.3 13.5 + - + +
88A ILE* 2.9 26.0 + - - +
100A SER* 5.8 0.9 - - - -
101A HIS* 3.8 37.7 - - + +
114A PHE* 3.5 30.3 - - + -
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Residues in contact with PRO 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ILE* 4.0 17.0 - - + -
69A PRO 5.9 0.4 - - - +
70A ARG* 6.2 0.2 - - - -
71A SER 6.2 1.1 - - - +
74A GLY 3.3 22.0 - - - +
75A ARG 5.0 0.7 - - - +
76A LEU* 4.3 15.7 - - + -
83A GLY 4.6 0.9 - - - +
84A LEU* 1.3 85.2 - - + +
86A HIS* 1.3 67.7 + - - +
88A ILE* 4.6 2.7 - - + -
89A TYR* 3.1 34.4 + - + +
114A PHE* 4.5 8.1 - - + -
121A VAL* 4.1 20.4 - - + -
123A ILE* 3.5 21.3 - - + +
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Residues in contact with HIS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.8 11.9 - - + +
85A PRO* 1.3 75.8 - - - +
87A VAL* 1.3 82.4 + - + +
89A TYR* 4.5 0.6 - - - +
90A CYS* 2.9 30.1 + - - +
101A HIS* 3.6 18.2 + - + +
104A LEU* 3.9 16.8 - - + -
114A PHE* 3.1 52.5 - + + +
121A VAL* 5.1 0.6 - - + +
122A CYS 4.2 2.2 + - - +
123A ILE* 4.0 9.3 - - - +
128A TYR* 3.5 49.1 - + + +
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Residues in contact with VAL 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LEU* 3.3 19.2 + - + +
85A PRO 3.2 0.6 - - - -
86A HIS* 1.3 90.8 - - + +
88A ILE* 1.3 66.3 + - + +
90A CYS* 3.8 1.4 - - - +
91A ARG* 3.1 44.8 + - - +
98A LEU* 4.0 14.7 - - + +
100A SER* 4.1 13.2 - - - +
101A HIS* 3.5 37.2 - - + +
104A LEU* 4.1 9.9 - - + -
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Residues in contact with ILE 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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30A TRP* 3.7 39.9 - - + -
34A ALA* 4.3 9.9 - - + -
76A LEU* 4.2 24.5 - - + +
78A VAL* 5.4 2.7 - - + -
81A ARG 5.6 0.7 - - - +
83A GLY* 3.9 26.2 - - - +
84A LEU 2.9 26.4 + - - +
85A PRO 3.7 4.0 - - - +
86A HIS 3.3 0.2 - - - -
87A VAL* 1.3 80.5 - - + +
89A TYR* 1.3 78.3 + - + +
91A ARG* 3.1 29.2 + - - +
92A VAL* 3.3 10.0 + - + +
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Residues in contact with TYR 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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34A ALA* 2.6 39.6 + - + +
35A VAL* 4.2 4.5 - - + -
37A ALA* 4.5 2.9 - - - +
38A LEU* 3.2 36.5 + - + +
41A LYS* 5.7 1.7 - - - -
68A ILE* 5.2 2.7 - - + -
76A LEU* 3.9 29.7 - - + +
78A VAL* 4.7 0.5 - - - +
85A PRO* 3.1 26.1 + - + +
86A HIS 4.5 0.7 - - - +
88A ILE* 1.3 81.8 - - + +
90A CYS* 1.3 64.8 + - - +
92A VAL* 3.3 8.4 + - + -
93A TRP* 3.2 57.4 + + + +
123A ILE* 4.1 31.4 - - + +
125A PRO* 4.1 2.0 - - - +
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Residues in contact with CYS 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 HIS* 2.9 23.4 + - - +
87A VAL 3.8 3.1 - - - +
89A TYR* 1.3 75.2 - - - +
91A ARG* 1.3 59.9 + - - +
94A ARG* 2.9 26.7 + - - -
95A TRP* 3.0 29.0 + - + -
98A LEU* 4.1 2.2 - - + -
104A LEU* 3.9 23.3 - - + -
123A ILE 5.8 0.9 - - - -
125A PRO* 3.7 37.5 - - - -
128A TYR* 4.4 10.5 - - - -
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Residues in contact with ARG 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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27A GLU* 5.5 9.2 + - - -
30A TRP* 5.7 5.3 - - - -
87A VAL* 3.1 28.9 + - - +
88A ILE* 3.1 27.9 + - - +
90A CYS* 1.3 75.4 - - - +
92A VAL* 1.3 68.5 + - + +
94A ARG 4.3 0.7 + - - -
95A TRP 3.3 19.2 - - - +
96A PRO* 3.4 37.5 - - - +
98A LEU* 2.7 33.1 + - + +
99A GLN* 3.7 18.8 + - - +
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Residues in contact with VAL 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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30A TRP* 5.7 2.5 - - + -
31A ALA* 4.7 20.0 - - + +
34A ALA* 5.3 2.2 - - + -
35A VAL* 4.0 24.7 - - + -
88A ILE* 3.3 20.6 + - + +
89A TYR* 3.7 16.8 - - + +
90A CYS 3.3 0.6 - - - -
91A ARG* 1.3 81.0 - - + +
93A TRP* 1.3 87.9 + - + +
96A PRO* 5.6 2.1 - - - +
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Residues in contact with TRP 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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35A VAL* 3.8 26.0 - - + +
38A LEU* 3.7 25.4 - - + -
52A LEU* 4.0 15.7 - - + -
56A LEU* 3.6 43.1 - - + +
89A TYR* 3.2 48.5 + + + +
92A VAL* 1.3 95.9 - - + +
94A ARG* 1.3 63.8 + - + +
96A PRO* 6.4 0.2 - - - -
123A ILE 5.2 0.7 - - - -
125A PRO* 3.6 20.9 - - + -
126A TYR* 4.5 6.6 + - + -
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Residues in contact with ARG 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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90A CYS 2.9 10.3 + - - +
92A VAL 3.7 0.6 - - - -
93A TRP* 1.3 84.6 - - + +
95A TRP* 1.3 111.1 + - + +
96A PRO* 3.4 11.5 - - - +
125A PRO* 3.3 38.0 + - + -
126A TYR* 3.1 44.5 + - + +
128A TYR 3.4 16.4 + - - -
129A LYS* 5.1 0.8 - - - +
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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