Contacts of the helix formed by residues 91 - 98 (chain W) in PDB entry 3EXG
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 91 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87W THR* 3.7 26.2 - - + -
88W ALA 3.8 9.0 - - - +
89W TYR 3.1 6.8 + - - -
90W ARG* 1.3 73.9 - - - +
92W HIS* 1.3 58.7 + - - +
93W GLY 3.4 1.8 - - - -
94W PHE* 3.9 3.6 - - - -
95W THR* 2.7 40.0 + - - +
123W SER 5.6 1.1 - - - +
124W MET 5.3 1.6 - - - +
126W MET* 4.4 6.3 - - + +
131W PHE* 3.9 13.5 - - + -
134W GLY* 4.0 12.1 - - - +
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Residues in contact with HIS 92 (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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45W MET* 4.5 13.8 - - - +
46W GLU* 3.0 32.3 + - - +
62W CYS* 4.4 4.9 - - - -
63W HIS 3.3 27.0 + - - -
64W LEU* 4.0 9.4 - - + -
89W TYR 5.0 1.8 + - - -
90W ARG 3.5 2.0 - - - -
91W ALA* 1.3 77.1 - - - +
93W GLY* 1.3 68.6 + - - +
94W PHE 3.2 0.3 + - - -
95W THR* 3.7 5.6 - - - -
96W PHE* 3.2 22.0 + - - +
105W ILE* 4.1 7.6 - - + +
109W LEU* 3.7 25.9 - - + +
123W SER* 2.9 29.5 + - - -
126W MET* 3.4 24.7 - - + -
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Residues in contact with GLY 93 (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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42W VAL* 3.9 13.9 - - - +
65W CYS* 3.7 26.8 - - - -
72W CYS* 3.9 17.7 - - - -
90W ARG 4.4 1.0 + - - -
91W ALA 3.4 0.2 - - - -
92W HIS* 1.3 80.1 - - - +
94W PHE* 1.3 58.2 + - - +
96W PHE* 3.5 3.6 + - - +
97W THR* 3.0 29.8 + - - +
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Residues in contact with PHE 94 (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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65W CYS* 6.3 0.4 - - - -
72W CYS* 3.5 35.0 - - + -
75W LEU* 3.8 18.6 - - + -
85W LEU* 3.9 27.1 - - + -
87W THR* 4.2 11.7 - - + -
90W ARG 4.0 16.4 - - - -
91W ALA* 3.5 5.8 + - - +
92W HIS 3.1 0.6 - - - -
93W GLY* 1.3 72.3 - - - +
95W THR* 1.3 66.9 + - - +
96W PHE 3.0 1.3 - - - -
97W THR* 3.0 11.8 + - - -
98W ARG* 2.9 29.8 + - - +
131W PHE* 3.8 19.3 - - + -
164W LEU* 3.2 34.3 - - + -
194W GLU* 3.6 18.4 - - - -
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Residues in contact with THR 95 (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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91W ALA* 2.7 28.2 + - - +
92W HIS 3.4 4.9 + - - -
94W PHE* 1.3 71.7 - - - +
96W PHE* 1.3 62.1 + - - +
98W ARG* 3.6 2.8 + - - +
99W GLY 3.5 4.0 + - - -
100W LEU* 3.1 63.0 + - + +
105W ILE* 3.6 15.5 - - + -
126W MET* 3.5 26.1 - - + +
127W TYR 5.1 0.9 - - - +
128W ALA* 4.9 1.1 - - + +
131W PHE* 3.8 22.4 - - + -
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Residues in contact with PHE 96 (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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38W MET* 4.0 26.0 - - + -
41W THR* 3.4 27.1 - - + -
42W VAL* 3.8 21.3 - - + -
45W MET* 4.4 5.8 - - + -
92W HIS 3.2 9.2 + - - +
93W GLY 3.6 7.4 - - - +
94W PHE 3.0 0.8 - - - -
95W THR* 1.3 74.9 - - - +
97W THR* 1.3 66.6 + - + +
98W ARG 2.8 10.8 + - - -
99W GLY* 2.9 14.4 + - - -
100W LEU 3.6 21.1 - - - +
101W SER* 5.2 1.1 - - - -
102W VAL* 3.6 34.3 - - + -
105W ILE* 3.7 7.6 - - + +
316W GLU* 5.1 4.9 - - - -
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Residues in contact with THR 97 (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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38W MET* 4.9 11.9 - - - +
42W VAL* 4.5 1.8 - - + -
72W CYS* 3.2 39.9 + - + +
73W VAL* 4.3 11.2 - - + -
76W GLU* 3.2 36.3 + - - +
93W GLY 3.0 16.2 - - - +
94W PHE* 3.0 15.1 + - - -
96W PHE* 1.3 86.9 - - + +
98W ARG* 1.3 59.0 + - - +
99W GLY 3.4 0.6 + - - -
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Residues in contact with ARG 98 (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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76W GLU* 2.7 42.5 + - - -
79W ILE* 3.5 11.3 - - - +
80W ASN 3.4 7.9 + - - -
81W PRO* 3.3 26.9 + - - +
83W ASP 2.7 24.3 + - - -
84W HIS* 4.3 1.2 - - - +
85W LEU* 4.3 14.0 - - - +
94W PHE* 2.9 17.1 + - - +
95W THR* 4.0 5.6 - - - +
96W PHE 2.8 0.6 + - - -
97W THR* 1.3 79.5 - - - +
99W GLY* 1.3 56.7 + - - +
100W LEU 4.0 0.4 - - - -
128W ALA* 4.8 6.3 - - + +
129W LYS* 3.9 15.6 + - - +
130W ASN* 3.0 27.2 + - - +
131W PHE* 3.5 38.1 - - + -
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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