Contacts of the helix formed by residues 87 - 99 (chain R) in PDB entry 6L49
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 87 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-132I T 5.6 2.5 - - - +
137J G 5.2 0.4 - - - +
44Q GLY* 4.4 13.9 - - - -
47Q ALA* 3.6 13.3 - - - +
83R ARG* 3.4 27.8 + - - +
85R THR* 4.4 9.2 - - + +
86R ILE* 1.3 78.7 - - - +
88R SER* 1.3 65.6 + - - +
89R ARG* 3.2 10.9 + - - +
90R GLU* 2.7 33.5 + - - -
91R ILE* 3.6 6.9 - - - +
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Residues in contact with SER 88 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46Q GLY* 3.3 28.0 + - - +
47Q ALA* 4.3 8.8 - - - +
50Q TYR* 4.2 8.2 - - - -
87R THR* 1.3 73.9 - - - +
89R ARG* 1.3 60.1 + - - +
91R ILE* 3.5 4.2 + - - +
92R GLN* 2.9 32.2 + - - +
115R VAL* 3.4 31.3 - - - +
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Residues in contact with ARG 89 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74P GLU 2.4 32.1 + - - -
75P HIS* 2.6 38.4 + - + -
77P LYS* 3.5 38.4 - - - +
83R ARG* 6.0 0.4 - - - +
87R THR* 3.2 10.2 + - - +
88R SER* 1.3 80.2 - - - +
90R GLU* 1.3 62.3 + - - +
92R GLN* 3.4 15.9 - - - +
93R THR* 2.9 32.2 + - + +
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Residues in contact with GLU 90 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75P HIS* 2.7 34.2 + - + +
74R ALA* 3.4 15.5 - - + +
78R ALA* 3.8 20.4 - - + -
83R ARG* 3.3 29.3 + - - -
85R THR 4.4 0.2 - - - -
86R ILE* 3.6 18.6 - - + -
87R THR* 2.7 41.2 + - - +
88R SER 3.3 0.4 - - - -
89R ARG* 1.3 78.2 + - - +
91R ILE* 1.3 59.8 + - - +
93R THR* 3.3 9.9 - - - +
94R ALA* 2.9 28.9 + - - +
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Residues in contact with ILE 91 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34Q LEU* 5.0 3.1 - - + -
47Q ALA* 3.7 20.2 - - + +
50Q TYR* 3.5 25.4 - - + -
51Q LEU* 3.7 44.0 - - + -
70R ILE* 3.8 11.2 - - + +
71R ALA* 5.0 3.8 - - - -
74R ALA* 3.7 20.9 - - + -
86R ILE* 3.7 14.8 - - + -
87R THR 3.6 15.3 - - - +
88R SER 3.5 3.1 + - - +
90R GLU* 1.3 74.7 - - - +
92R GLN* 1.3 56.3 + - - +
94R ALA* 3.6 1.4 - - - +
95R VAL* 2.9 30.1 + - + +
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Residues in contact with GLN 92 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q TYR* 3.4 25.0 + - + +
88R SER* 2.9 23.3 + - - +
89R ARG* 3.4 18.2 - - - +
91R ILE* 1.3 77.4 - - - +
93R THR* 1.3 57.9 + - - +
95R VAL* 3.3 4.7 + - - +
96R ARG* 2.9 54.9 + - - +
108R VAL* 4.1 2.3 - - + +
112R THR* 3.9 24.9 - - - +
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Residues in contact with THR 93 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71P THR* 3.4 28.4 + - - +
75P HIS* 3.5 32.6 - - + +
77R LEU* 3.7 18.8 - - + +
89R ARG* 2.9 22.4 + - - +
90R GLU* 3.3 11.7 - - - +
92R GLN* 1.3 74.8 - - - +
94R ALA* 1.3 59.4 + - - +
96R ARG* 3.7 8.8 - - - +
97R LEU* 2.9 30.5 + - - +
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Residues in contact with ALA 94 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70R ILE* 3.6 31.0 - - + +
73R GLU* 3.8 9.6 - - + -
74R ALA* 3.7 14.6 - - + +
77R LEU* 3.8 7.6 - - + -
90R GLU 2.9 19.0 + - - +
91R ILE 3.6 4.9 - - - +
92R GLN 3.3 0.2 - - - -
93R THR* 1.3 76.4 - - - +
95R VAL* 1.3 60.6 + - - +
97R LEU* 3.4 0.7 + - - +
98R LEU* 2.9 34.7 + - - +
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Residues in contact with VAL 95 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50Q TYR* 3.8 7.6 - - + +
54Q VAL* 3.8 24.9 - - + -
70R ILE* 3.9 26.5 - - + -
91R ILE* 2.9 20.9 + - + +
92R GLN 3.6 3.6 - - - +
94R ALA* 1.3 75.3 - - - +
96R ARG* 1.3 58.4 + - - +
98R LEU* 5.0 0.2 - - - -
99R LEU* 3.0 40.8 + - + +
104R ALA* 3.6 14.1 - - - +
107R ALA* 3.7 26.0 - - + -
108R VAL* 4.3 7.9 - - + +
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Residues in contact with ARG 96 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67P ARG* 6.0 2.4 - - - -
68P ASP* 5.7 0.2 - - - +
71P THR* 4.1 20.4 + - + +
74P GLU* 6.2 0.2 - - - -
92R GLN* 2.9 40.8 + - - +
93R THR* 3.8 9.9 - - - +
94R ALA 3.3 0.2 - - - -
95R VAL* 1.3 76.9 - - - +
97R LEU* 1.3 60.8 + - - +
99R LEU 3.8 9.2 - - - +
104R ALA* 4.0 11.5 - - + +
105R LYS* 6.0 4.6 - - - +
108R VAL* 3.5 44.9 - - + +
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Residues in contact with LEU 97 (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 52.5 - - + +
71P THR* 3.8 15.5 - - + +
72P TYR* 3.6 31.0 - - + +
92P ARG* 3.0 26.1 + - + +
73R GLU* 4.3 9.6 - - + +
77R LEU* 3.7 25.8 - - + -
93R THR* 2.9 23.8 + - - +
94R ALA* 3.9 3.6 - - - +
96R ARG* 1.3 78.7 - - - +
98R LEU* 1.3 64.1 + - - +
99R LEU 4.3 1.6 - - - +
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Residues in contact with LEU 98 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92P ARG* 3.3 34.8 + - + +
96Q LEU* 4.9 8.9 - - + +
69R ARG* 3.6 44.9 - - + +
70R ILE* 3.8 19.1 - - + -
73R GLU* 3.8 27.4 - - + +
94R ALA 2.9 16.2 + - - +
95R VAL 4.5 0.2 - - - +
97R LEU* 1.3 77.7 - - - +
99R LEU* 1.3 73.0 + - + +
100R PRO* 3.7 4.5 - - - +
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Residues in contact with LEU 99 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54Q VAL* 4.5 12.6 - - + -
58Q LEU* 4.4 9.9 - - + -
96Q LEU* 3.8 31.2 - - + -
66R ILE* 5.6 0.7 - - + -
70R ILE* 4.8 9.4 - - + -
95R VAL* 3.0 40.0 + - + +
96R ARG 3.8 8.7 - - - +
97R LEU 4.3 1.6 - - - +
98R LEU* 1.3 81.3 - - + +
100R PRO* 1.3 70.8 - - + +
103R LEU* 3.8 25.8 - - + +
104R ALA* 3.4 19.8 - - + +
107R ALA* 3.9 17.0 - - + -
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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