Contacts of the helix formed by residues 91 - 98 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87O THR* 3.7 24.7 - - + -
89O TYR 3.1 7.7 + - - +
90O ARG* 1.3 73.6 - - - +
92O HIS* 1.3 65.6 + - - +
93O GLY 3.5 1.6 - - - -
94O PHE* 4.0 5.4 - - - -
95O THR* 2.7 36.6 + - - +
123O SER 5.2 2.9 - - - +
124O MET 5.6 0.4 - - - +
126O MET* 4.3 6.3 - - + +
131O PHE* 3.8 8.3 - - + -
134O GLY* 3.8 22.4 - - - +
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Residues in contact with HIS 92 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45O MET* 4.7 10.4 - - - +
46O GLU* 3.1 39.8 + - - +
49O ALA* 4.9 0.2 - - - +
62O CYS* 3.9 24.0 - - - -
63O HIS 3.7 16.6 + - - -
64O LEU* 4.2 2.6 - - + +
65O CYS* 5.0 0.4 - - - -
89O TYR 5.2 1.0 + - - -
90O ARG 3.6 2.4 - - - -
91O ALA* 1.3 78.4 - - - +
93O GLY* 1.3 67.4 + - - +
95O THR* 3.0 14.3 + - - -
96O PHE* 3.2 9.7 + - - +
105O ILE* 4.1 9.3 - - + +
109O LEU* 3.8 20.6 - - + +
123O SER* 2.7 30.4 + - - -
126O MET* 3.6 25.1 - - + -
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Residues in contact with GLY 93 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42O VAL* 3.8 31.6 - - - +
65O CYS* 3.6 13.9 - - - -
72O CYS* 3.9 13.7 - - - -
90O ARG 5.0 0.4 + - - -
92O HIS* 1.3 78.1 - - - +
94O PHE* 1.3 58.1 + - - +
96O PHE* 3.1 5.2 + - - +
97O THR* 3.1 31.0 + - - +
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Residues in contact with PHE 94 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65O CYS* 6.2 2.0 - - + -
71O CYS* 4.1 4.3 - - + -
72O CYS* 3.7 35.7 - - + -
75O LEU* 3.9 12.1 - - + -
76O GLU* 5.9 0.7 - - - -
85O LEU* 3.5 39.5 - - + -
87O THR* 4.8 8.5 - - + -
90O ARG 4.3 15.5 - - - -
91O ALA* 3.6 6.0 + - - +
92O HIS 3.1 0.6 - - - -
93O GLY* 1.3 73.0 - - - +
95O THR* 1.3 66.5 + - - +
96O PHE 3.1 1.9 + - - -
97O THR* 3.4 8.7 + - - -
98O ARG* 3.1 29.2 + - + +
131O PHE* 4.0 20.0 - + + -
164O LEU* 3.2 32.5 - - + -
194O GLU* 3.9 15.5 - - - -
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Residues in contact with THR 95 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91O ALA* 2.7 26.4 + - - +
92O HIS 3.0 5.6 + - - -
94O PHE* 1.3 76.7 - - - +
96O PHE* 1.3 62.6 + - - +
98O ARG* 3.6 4.9 + - - +
99O GLY 3.6 0.9 + - - -
100O LEU* 3.2 55.5 + - + +
105O ILE* 3.6 15.9 - - + -
126O MET* 3.5 24.0 - - + +
127O TYR 5.1 0.2 - - - +
128O ALA* 4.8 3.7 - - + +
131O PHE* 3.7 20.8 - - + -
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Residues in contact with PHE 96 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37O ARG* 6.2 1.3 - - + -
38O MET* 3.7 28.5 - - + -
41O THR* 3.5 31.4 - - + -
42O VAL* 3.8 25.4 - - + -
45O MET* 4.8 3.1 - - + -
92O HIS 3.2 5.8 + - - +
93O GLY 3.1 8.6 + - - +
94O PHE 3.1 0.4 - - - -
95O THR* 1.3 72.5 - - - +
97O THR* 1.3 64.7 + - + +
98O ARG 2.7 15.5 + - - -
99O GLY* 2.9 12.6 + - - -
100O LEU 3.6 23.4 - - - +
101O SER* 4.8 2.2 - - - -
102O VAL* 4.1 24.0 - - + -
105O ILE* 3.7 9.8 - - + +
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Residues in contact with THR 97 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38O MET* 4.5 13.3 - - - +
42O VAL* 4.6 1.6 - - + -
72O CYS* 3.8 39.3 + - - +
73O VAL* 4.1 13.9 - - + +
76O GLU* 3.2 34.4 + - - +
93O GLY 3.1 13.4 + - - +
94O PHE* 3.4 19.4 + - - -
96O PHE* 1.3 85.6 - - + +
98O ARG* 1.3 57.6 + - - +
99O GLY 3.6 0.4 - - - -
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Residues in contact with ARG 98 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76O GLU* 3.1 26.2 + - - +
79O ILE* 3.3 16.7 - - - +
80O ASN 2.7 30.5 + - - -
81O PRO* 3.5 9.8 + - - +
83O ASP 2.5 25.4 + - - -
85O LEU* 4.1 16.6 - - + +
94O PHE* 3.1 19.6 + - + +
95O THR 4.0 3.8 - - - +
96O PHE 2.7 7.5 + - - -
97O THR* 1.3 77.5 - - - +
99O GLY* 1.3 55.0 + - - -
100O LEU 3.9 1.3 - - - -
128O ALA* 4.3 8.0 - - + +
129O LYS* 3.6 21.5 + - - +
130O ASN* 2.9 28.8 + - - +
131O PHE* 3.7 33.4 - - + -
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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