Contacts of the helix formed by residues 85 - 99 (chain W) in PDB entry 5GJQ
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 85 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11W ASP* 4.8 0.2 + - - -
54W LEU* 2.0 51.9 + - - +
55W ALA 1.9 36.1 + - - +
58W CYS* 3.5 16.4 - - - +
84W ILE* 1.3 74.0 - - - +
86W PHE* 1.3 55.8 + - - +
87W CYS* 3.4 1.8 - - - -
88W THR* 2.8 12.9 + - - -
89W GLY 2.3 30.5 + - - -
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Residues in contact with PHE 86 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9W CYS* 5.2 13.7 - - - -
11W ASP* 5.0 12.3 + - - +
54W LEU* 3.6 5.2 - - - +
84W ILE* 3.2 19.9 - - + +
85W THR* 1.3 74.3 - - - +
87W CYS* 1.3 56.7 + - - +
89W GLY* 4.2 0.7 - - - +
90W ILE* 2.2 48.3 + - + +
111W ALA* 5.9 5.2 - - + -
113W VAL* 6.0 5.4 - - + -
115W SER* 5.4 0.7 - - - +
117W VAL* 6.2 4.0 - - + -
119W ASP* 6.3 1.6 - - + -
153W LEU* 5.7 9.6 - - + -
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Residues in contact with CYS 87 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84W ILE* 4.8 2.0 - - + +
85W THR 3.4 0.4 - - - -
86W PHE* 1.3 77.2 - - - +
88W THR* 1.3 53.1 + - - +
90W ILE* 3.4 2.3 - - - +
91W ARG* 2.4 40.0 + - - +
118W GLU 5.8 0.9 - - - +
119W ASP* 3.6 30.1 + - + +
123W ASP* 4.3 11.0 - - - -
127W LEU* 3.7 23.7 - - + +
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Residues in contact with THR 88 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66U SER* 6.1 0.2 - - - -
67U VAL* 3.3 31.3 - - + +
58W CYS* 3.7 29.8 - - + -
85W THR* 2.8 14.3 + - - -
87W CYS* 1.3 76.8 - - - +
89W GLY* 1.3 52.5 + - - +
91W ARG* 3.0 7.5 + - - +
92W VAL* 2.5 42.0 + - + +
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Residues in contact with GLY 89 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9W CYS* 5.7 0.2 - - - -
52W ILE* 3.4 23.4 - - - +
53W THR 5.5 0.4 - - - -
54W LEU* 4.2 9.9 - - - -
58W CYS* 4.8 3.6 - - - -
85W THR* 2.3 26.1 + - - -
86W PHE* 3.2 3.4 - - - -
88W THR* 1.3 67.3 - - - +
90W ILE* 1.3 50.4 + - - +
92W VAL* 3.1 9.8 - - - +
93W ALA* 2.5 35.5 + - - +
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Residues in contact with ILE 90 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9W CYS* 5.4 4.1 - - - -
52W ILE* 5.1 0.4 - - - -
86W PHE* 2.2 39.0 + - + +
87W CYS* 3.4 5.6 - - - +
89W GLY 1.3 67.0 - - - +
91W ARG* 1.3 51.9 + - - +
93W ALA* 2.8 10.2 + - - +
94W HIS* 2.5 50.4 + - + -
109W ILE* 4.3 19.1 - - + -
127W LEU* 4.7 13.7 - - + -
131W LEU* 4.4 13.5 - - + -
138W VAL* 6.1 0.9 - - + -
156W PHE* 4.9 6.7 - - + -
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Residues in contact with ARG 91 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61U ASP* 3.4 35.0 - - - +
67U VAL* 4.1 4.9 - - + -
87W CYS 2.4 27.3 + - - +
88W THR* 3.4 9.6 - - - +
90W ILE* 1.3 71.7 - - - +
92W VAL* 1.3 60.8 + - - +
94W HIS* 3.4 12.9 - - + +
95W LEU* 3.1 29.3 + - + +
127W LEU* 4.0 16.1 - - + +
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Residues in contact with VAL 92 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67U VAL* 4.2 21.5 - - + -
68U TRP 4.4 10.8 - - - +
69U PHE* 4.9 4.6 - - + -
52W ILE* 5.4 7.4 - - + -
58W CYS* 5.1 6.7 - - + -
59W GLU* 5.7 6.7 - - - +
60W VAL* 5.8 5.4 - - + -
88W THR* 2.5 28.8 + - + +
89W GLY* 3.1 11.0 - - - +
91W ARG* 1.3 70.6 - - - +
93W ALA* 1.3 55.9 + - - +
95W LEU* 2.9 11.1 + - - +
96W ALA* 2.5 37.3 + - - +
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Residues in contact with ALA 93 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7W MET* 3.6 27.5 - - + +
9W CYS* 5.7 0.2 - - + -
52W ILE* 4.2 8.4 - - + +
89W GLY 2.5 18.4 + - - +
90W ILE* 2.8 16.3 + - - +
92W VAL* 1.3 70.9 - - - +
94W HIS* 1.3 54.6 + - - +
96W ALA* 3.1 10.7 - - - +
97W LEU* 3.0 32.9 + - - +
109W ILE* 3.8 19.5 - - + -
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Residues in contact with HIS 94 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90W ILE* 2.5 32.7 + - + -
91W ARG* 3.4 13.2 - - + +
93W ALA* 1.3 68.8 - - - +
95W LEU* 1.3 59.6 + - + +
97W LEU* 2.8 29.4 + - - +
98W LYS* 2.8 23.8 + - - +
109W ILE* 4.5 3.6 - - + -
127W LEU* 5.5 4.5 - - + -
130W ARG* 5.1 15.3 - - + -
131W LEU* 3.6 32.5 - - + -
134W GLU* 5.5 3.1 - - + -
136W VAL* 5.0 5.4 - - + -
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Residues in contact with LEU 95 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59U ASP* 3.7 16.8 - - + +
60U GLU 4.2 4.3 - - - +
61U ASP* 4.2 20.6 - - - +
67U VAL* 4.1 10.5 - - + -
68U TRP* 3.6 37.7 - - - +
69U PHE* 3.6 22.2 - - + +
91W ARG* 3.1 16.4 + - + +
92W VAL* 2.9 9.2 + - - +
94W HIS* 1.3 77.2 - - + +
96W ALA* 1.3 66.6 + - - +
98W LYS* 2.9 53.5 + - + +
99W HIS* 3.2 6.1 + - - -
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Residues in contact with ALA 96 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69U PHE* 4.0 29.9 - - + -
7W MET* 5.3 7.0 - - + -
50W GLY* 6.1 3.1 - - - -
52W ILE* 5.5 1.6 - - + -
60W VAL* 5.3 5.8 - - + -
63W THR* 5.8 3.8 - - + -
92W VAL 2.5 17.4 + - - +
93W ALA* 3.1 18.4 - - - +
95W LEU* 1.3 69.3 - - - +
97W LEU* 1.3 56.0 - - + +
99W HIS* 2.7 30.8 + - - +
100W ARG* 3.2 7.0 + - - -
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Residues in contact with LEU 97 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5W SER* 3.6 31.9 - - - +
6W THR 3.7 12.3 - - - +
7W MET* 4.8 2.7 - - + -
93W ALA 3.0 10.0 + - - +
94W HIS* 2.8 11.3 + - - +
96W ALA* 1.3 77.2 - - + +
98W LYS* 1.3 60.8 + - - +
99W HIS 3.1 0.2 - - - -
100W ARG* 2.8 37.9 + - + +
107W MET* 3.4 31.6 - - + -
108W ARG 3.1 29.6 - - - +
109W ILE* 3.4 20.2 - - + -
136W VAL* 3.5 9.4 - - + -
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Residues in contact with LYS 98 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59U ASP* 4.1 16.8 - - + -
60U GLU 5.0 1.8 + - - -
62U ASP* 5.4 4.6 - - - +
94W HIS* 2.8 18.9 + - - +
95W LEU* 2.9 45.9 + - + +
97W LEU* 1.3 76.5 - - + +
99W HIS* 1.3 63.5 + - + +
100W ARG* 3.4 5.1 + - - +
103W LYS* 4.2 18.2 + - - +
130W ARG* 5.2 7.5 - - - +
134W GLU* 3.9 29.0 - - + +
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Residues in contact with HIS 99 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57U PRO* 3.3 37.2 + - + +
58U PHE* 3.2 32.6 + - - -
59U ASP* 3.6 12.4 + - + +
69U PHE* 3.7 34.5 - + + -
71U ASP* 5.2 3.6 - - + +
101V GLN* 4.2 9.2 + - + +
95W LEU 3.2 5.0 + - - -
96W ALA 2.7 17.1 + - - +
98W LYS* 1.3 74.5 + - - +
100W ARG* 1.3 57.5 + - - +
101W GLN* 2.4 38.6 + - - +
103W LYS* 4.9 2.9 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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