Contacts of the helix formed by residues 91 - 98 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87S THR* 3.6 25.8 - - + -
88S ALA 4.3 0.9 - - - +
89S TYR 3.3 5.5 + - - -
90S ARG* 1.3 74.8 - - - +
92S HIS* 1.3 63.8 + - - +
93S GLY 3.3 2.7 - - - +
94S PHE* 3.5 5.3 + - - -
95S THR* 2.7 40.2 + - - +
123S SER 5.6 1.8 + - - +
124S MET 5.5 1.1 - - - +
126S MET* 4.7 6.3 - - + +
131S PHE* 3.7 14.8 - - + -
134S GLY* 4.0 14.1 - - - +
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Residues in contact with HIS 92 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42S VAL* 5.3 0.2 - - - -
45S MET* 4.5 14.7 - - - +
46S GLU* 3.0 38.5 + - - +
62S CYS* 4.3 9.0 - - - -
63S HIS 3.4 22.6 + - - -
64S LEU* 4.4 0.2 - - + -
65S CYS* 5.0 0.2 - - - -
89S TYR 5.1 1.0 + - - -
90S ARG 3.7 2.0 - - - -
91S ALA* 1.3 78.9 + - - +
93S GLY* 1.3 70.4 + - - +
95S THR* 3.4 5.1 + - - -
96S PHE* 3.2 20.8 + - - +
105S ILE* 3.9 10.0 - - + +
109S LEU* 3.8 26.2 - - + +
123S SER* 3.0 28.3 + - - -
126S MET* 3.3 25.9 - - + +
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Residues in contact with GLY 93 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42S VAL* 3.9 10.9 - - - +
65S CYS* 3.5 20.4 - - - +
72S CYS* 3.7 26.2 - - - -
90S ARG 5.1 0.2 + - - -
91S ALA 3.3 0.4 - - - -
92S HIS* 1.3 80.0 - - - +
94S PHE* 1.3 63.3 + - - +
96S PHE* 3.2 2.9 + - - +
97S THR* 3.1 24.3 + - - +
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Residues in contact with PHE 94 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65S CYS* 6.5 0.9 - - + -
72S CYS* 3.6 34.5 - - + -
75S LEU* 3.9 19.5 - - + -
76S GLU* 5.7 0.7 - - - -
85S LEU* 3.3 35.0 - - + -
87S THR* 4.5 13.9 - - + -
90S ARG 4.4 18.8 - - - -
91S ALA* 3.5 1.5 + - - +
92S HIS 3.3 0.4 - - - -
93S GLY* 1.3 74.1 - - - +
95S THR* 1.3 69.5 + - - +
96S PHE 3.0 0.2 + - - -
97S THR* 3.1 10.5 + - - +
98S ARG* 2.9 27.7 + - + +
131S PHE* 3.9 11.0 - - + -
164S LEU* 3.3 31.0 - - + -
194S GLU* 4.3 15.3 - - - -
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Residues in contact with THR 95 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91S ALA* 2.7 22.9 + - - +
92S HIS* 3.8 2.2 - - - -
94S PHE* 1.3 77.0 - - - +
96S PHE* 1.3 61.5 + - - +
98S ARG* 3.5 6.0 + - - +
99S GLY 3.6 0.5 + - - -
100S LEU* 3.1 63.0 + - + +
105S ILE* 3.5 17.0 - - + -
126S MET* 3.9 21.7 - - + +
131S PHE* 3.2 25.8 - - + -
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Residues in contact with PHE 96 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38S MET* 3.7 27.6 - - + -
41S THR* 3.5 27.6 - - + -
42S VAL* 3.6 22.7 - - + -
45S MET* 4.5 4.9 - - + -
92S HIS 3.2 7.8 + - - +
93S GLY 3.2 7.4 + - - +
94S PHE 3.0 0.8 - - - -
95S THR* 1.3 75.1 - - - +
97S THR* 1.3 65.6 + - + +
98S ARG 2.8 11.6 + - - -
99S GLY* 3.0 11.6 + - - -
100S LEU 3.5 21.6 - - - +
101S SER* 5.3 1.3 - - - -
102S VAL* 3.8 27.8 - - + -
105S ILE* 3.5 8.9 - - + +
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Residues in contact with THR 97 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38S MET* 4.9 12.0 - - + +
42S VAL* 4.5 1.6 - - + -
72S CYS* 3.4 33.5 + - + +
73S VAL* 4.3 14.4 - - + +
76S GLU* 2.9 40.6 + - + +
93S GLY 3.1 12.1 + - - +
94S PHE* 3.1 19.9 + - - +
96S PHE* 1.3 87.6 - - + +
98S ARG* 1.3 56.0 + - - +
99S GLY 3.4 0.7 - - - -
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Residues in contact with ARG 98 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76S GLU* 3.0 29.8 + - - +
79S ILE* 3.2 16.0 - - - +
80S ASN 2.7 29.7 + - - -
81S PRO* 3.7 10.0 + - - +
83S ASP 3.1 19.0 + - - -
85S LEU* 4.4 19.3 - - + +
94S PHE 2.9 20.3 + - - +
95S THR 4.0 2.7 - - - +
96S PHE 2.8 3.0 + - - -
97S THR* 1.3 75.7 - - - +
99S GLY* 1.3 57.9 + - - +
100S LEU 3.9 1.6 - - - -
128S ALA* 4.3 8.0 - - + +
129S LYS* 3.6 20.4 + - - +
130S ASN* 2.7 44.6 + - - +
131S PHE* 3.8 22.4 - - + -
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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