Contacts of the helix formed by residues 90 - 102 (chain R) in PDB entry 6M44
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 90 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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230J A 6.5 0.4 - - - -
231J G 5.8 3.8 - - - +
44Q GLY* 4.1 11.7 - - - -
47Q ALA* 3.8 4.5 - - - -
86R ARG* 6.3 1.1 - - - -
88R THR* 4.2 21.1 - - + +
89R ILE* 1.3 75.9 - - - +
91R SER* 1.3 60.5 + - - +
92R ARG* 2.9 19.3 + - - +
93R GLU* 2.6 42.0 + - - +
94R ILE* 3.3 13.0 + - - +
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Residues in contact with SER 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44Q GLY 5.3 0.2 - - - -
46Q GLY* 3.3 24.9 + - - -
47Q ALA* 3.5 24.0 - - - +
50Q TYR* 4.2 11.8 - - - -
90R THR* 1.3 73.3 - - - +
92R ARG* 1.3 56.1 + - - +
94R ILE* 3.6 4.9 + - - +
95R GLN* 3.1 27.0 + - - +
118R VAL* 4.2 19.2 - - - +
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Residues in contact with ARG 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74P GLU 3.6 19.0 + - - -
75P HIS* 2.9 42.9 + - + +
77P LYS* 4.0 30.7 - - - +
90R THR* 2.9 16.8 + - - +
91R SER* 1.3 75.0 + - - +
93R GLU* 1.3 68.0 + - - +
95R GLN* 3.3 9.1 + - + +
96R THR* 3.1 27.6 + - - +
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Residues in contact with GLU 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75P HIS* 3.5 32.8 + - + +
77R ALA* 4.3 13.7 - - + +
80R LEU* 4.4 11.3 - - + +
81R ALA* 4.5 9.2 - - - +
86R ARG* 3.9 25.1 - - - +
88R THR 4.0 6.9 - - - +
89R ILE* 4.1 14.8 - - + -
90R THR* 2.6 49.1 + - - +
92R ARG* 1.3 74.5 - - - +
94R ILE* 1.3 66.7 + - - +
96R THR* 3.1 5.0 + - - -
97R ALA* 2.9 22.9 + - - +
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Residues in contact with ILE 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Q LEU* 5.4 6.7 - - + -
47Q ALA* 3.6 31.9 - - + +
50Q TYR* 3.4 24.2 - - + -
51Q LEU* 4.0 31.4 - - + +
73R ILE* 4.2 22.0 - - + -
74R ALA* 5.4 2.5 - - - +
77R ALA* 4.3 6.7 - - + -
89R ILE* 4.1 17.9 - - + -
90R THR 3.3 4.7 + - - +
91R SER* 3.6 7.2 - - - +
93R GLU* 1.3 74.9 - - - +
95R GLN* 1.3 66.2 + - - +
97R ALA* 3.3 6.9 - - - +
98R VAL* 3.0 23.5 + - + +
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Residues in contact with GLN 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q TYR* 2.6 46.6 + - - +
91R SER 3.1 15.0 + - - +
92R ARG* 3.4 11.9 - - - +
93R GLU 3.2 0.2 - - - -
94R ILE* 1.3 74.0 - - - +
96R THR* 1.3 66.0 + - - +
98R VAL* 2.8 17.9 + - - +
99R ARG* 3.0 34.3 + - - +
111R VAL* 4.1 15.0 - - + +
115R THR* 3.4 14.1 + - - -
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Residues in contact with THR 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P THR* 3.8 20.9 - - + +
75P HIS* 2.8 51.2 + - + +
80R LEU* 4.1 13.2 - - + -
92R ARG* 3.1 9.8 + - - +
93R GLU 3.1 7.0 + - - -
95R GLN* 1.3 76.5 - - - +
97R ALA* 1.3 64.0 + - - +
99R ARG* 3.1 20.2 + - - +
100R LEU* 3.1 17.1 + - + +
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Residues in contact with ALA 97 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73R ILE* 4.0 18.2 - - + +
76R GLU* 4.1 16.2 - - + -
77R ALA* 3.9 25.4 - - - +
80R LEU* 4.6 2.4 - - + +
93R GLU 2.9 12.2 + - - +
94R ILE* 3.3 10.8 - - - +
96R THR* 1.3 75.1 - - - +
98R VAL* 1.3 53.1 + - - +
100R LEU* 2.9 25.9 + - - +
101R LEU* 2.9 19.3 + - - +
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Residues in contact with VAL 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q TYR* 4.6 2.5 - - + -
54Q VAL* 4.1 19.5 - - + -
73R ILE* 3.8 27.4 - - + -
94R ILE* 3.0 22.2 + - + +
95R GLN* 2.8 15.1 + - - +
97R ALA* 1.3 70.2 - - - +
99R ARG* 1.3 56.1 + - - +
101R LEU* 4.4 5.4 - - - +
102R LEU* 2.8 55.4 + - + +
107R ALA* 4.6 2.5 - - - -
110R ALA* 3.9 15.7 - - + -
111R VAL* 4.5 15.0 - - + +
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Residues in contact with ARG 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P ARG* 5.8 4.2 - - - -
68P ASP* 5.2 1.6 - - - +
71P THR* 4.3 17.9 - - + -
74P GLU* 6.1 0.9 - - - -
95R GLN* 3.0 36.0 + - - +
96R THR* 3.3 13.2 - - - +
98R VAL* 1.3 76.1 - - - +
100R LEU* 1.3 61.7 + - - +
102R LEU 3.6 11.8 - - - +
107R ALA* 4.6 11.7 - - + +
108R LYS* 6.1 1.4 - - - +
111R VAL* 4.1 32.8 - - + +
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Residues in contact with LEU 100 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68P ASP* 3.7 35.4 - - + +
71P THR* 3.3 32.1 - - + -
72P TYR* 3.7 34.1 - - + +
92P ARG* 3.2 32.3 + - - +
95Q LYS* 5.9 1.0 + - - -
76R GLU* 4.0 16.4 - - + +
80R LEU* 4.1 10.5 - - + -
96R THR* 3.1 17.7 + - + +
97R ALA* 2.9 7.7 + - - +
99R ARG* 1.3 77.4 - - - +
101R LEU* 1.3 59.3 + - - +
102R LEU 4.5 1.7 - - - +
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Residues in contact with LEU 101 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92P ARG* 4.0 17.1 + - - +
95Q LYS* 5.3 4.2 + - - -
96Q LEU* 4.1 11.9 - - + +
72R ARG* 3.3 64.9 + - + +
73R ILE* 3.5 21.1 - - + +
76R GLU* 3.9 14.6 - - + +
97R ALA 2.9 17.4 + - - +
98R VAL* 4.1 2.7 - - - +
100R LEU* 1.3 79.1 - - - +
102R LEU* 1.3 73.1 + - + +
103R PRO* 4.1 1.9 - - - +
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Residues in contact with LEU 102 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q VAL* 4.6 2.7 - - + -
58Q LEU* 4.0 28.0 - - + -
95Q LYS* 5.2 2.7 + - - -
96Q LEU* 3.7 31.2 - - + -
69R ILE* 5.3 6.7 - - + -
73R ILE* 5.7 2.7 - - + -
98R VAL* 2.8 30.5 + - + +
99R ARG 3.6 14.7 - - - +
100R LEU 4.5 1.6 - - - +
101R LEU* 1.3 80.7 - - + +
103R PRO* 1.4 67.8 - - + +
104R GLY 3.9 0.5 + - - -
106R LEU* 4.0 8.7 - - + +
107R ALA* 4.0 16.2 - - + +
110R ALA* 3.7 29.6 - - + -
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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