Contacts of the helix formed by residues 82 - 93 (chain X) 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 82 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198I G 5.2 10.1 - - - +
199I A 5.9 1.3 - - - +
85W GLN* 3.5 30.3 - - + +
88W ALA* 3.9 3.1 - - - +
78X ARG* 3.3 35.2 + - - +
80X THR* 3.1 11.3 + - + +
81X VAL* 1.3 86.7 - - - +
83X ALA* 1.3 64.1 + - - +
84X MET* 3.5 19.5 + - - +
85X ASP* 3.6 11.1 + - - +
86X VAL* 3.8 7.1 - - - +
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Residues in contact with ALA 83 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85W GLN* 3.6 8.0 + - - +
87W SER* 3.6 29.2 - - - +
88W ALA* 3.7 23.2 - - - +
91W ALA* 5.6 1.3 - - + -
82X THR* 1.3 74.3 - - - +
84X MET* 1.3 63.2 + - + +
86X VAL* 3.0 6.3 + - + +
87X VAL* 3.0 32.6 + - + +
100X PHE* 4.8 11.0 - - + +
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Residues in contact with MET 84 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78X ARG* 5.6 1.6 - - - +
82X THR* 3.3 14.5 - - - +
83X ALA* 1.3 80.5 - - + +
85X ASP* 1.3 58.4 + - - +
87X VAL* 3.3 4.7 + - + +
88X TYR* 2.9 69.7 + - + +
100X PHE 3.9 17.5 - - - +
101X GLY* 3.4 24.5 - - - +
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Residues in contact with ASP 85 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X ALA* 3.6 23.2 - - + +
72X TYR* 3.5 30.8 - - + +
73X THR* 2.5 25.8 + - - +
78X ARG* 2.8 36.0 + - - -
81X VAL* 3.9 0.8 - - + +
82X THR* 3.6 14.6 + - - +
83X ALA 3.2 0.4 - - - -
84X MET* 1.3 78.5 - - - +
86X VAL* 1.3 57.5 + - - +
88X TYR* 3.4 5.1 + - - -
89X ALA* 2.9 29.5 + - - +
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Residues in contact with VAL 86 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88W ALA* 3.8 35.7 - - + +
91W ALA* 4.4 6.5 - - + -
92W LEU* 3.8 41.7 - - + +
65X VAL* 4.6 4.7 - - + -
69X ALA* 4.5 13.9 - - + -
81X VAL* 5.1 2.7 - - + -
82X THR 3.8 7.6 - - - +
83X ALA* 3.0 6.9 + - - +
85X ASP* 1.3 75.2 - - - +
87X VAL* 1.3 60.6 + - - +
89X ALA* 3.3 6.0 + - - +
90X LEU* 2.9 41.4 + - + +
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Residues in contact with VAL 87 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91W ALA* 5.6 3.8 - - + -
83X ALA* 3.0 16.9 + - + +
84X MET* 3.8 8.7 - - + +
86X VAL* 1.3 77.5 - - + +
88X TYR* 1.3 65.5 + - + +
90X LEU* 3.3 9.6 + - + +
91X LYS* 2.9 31.0 + - + +
96X THR* 4.8 5.9 + - - +
97X LEU* 4.4 18.2 - - + +
100X PHE* 3.7 37.7 - - + +
101X GLY 4.8 2.9 - - - +
102X GLY* 4.4 23.8 - - - +
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Residues in contact with TYR 88 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72X TYR* 3.4 29.7 + + + -
84X MET* 2.9 55.1 + - + +
85X ASP* 4.5 7.9 - - - -
87X VAL* 1.3 84.7 - - + +
89X ALA* 1.3 58.6 + - - +
91X LYS* 3.7 9.3 - - + +
92X ARG* 2.9 28.2 + - - +
102X GLY* 6.4 1.3 - - - -
80Z TYR* 3.4 73.7 + + + +
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Residues in contact with ALA 89 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65X VAL* 3.9 22.9 - - + +
68X ASP* 3.7 27.5 - - + +
69X ALA 4.3 0.9 - - - +
72X TYR* 3.4 8.2 - - + -
85X ASP 2.9 18.5 + - - +
86X VAL* 3.7 5.8 - - - +
88X TYR* 1.3 77.6 - - - +
90X LEU* 1.3 58.0 + - - +
92X ARG* 3.4 4.5 + - - +
93X GLN* 3.0 34.6 + - - +
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Residues in contact with LEU 90 (chain X).
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* 4.6 2.2 - - + +
95W ALA* 3.7 33.0 - - + -
61X PHE* 4.7 13.7 - - + -
65X VAL* 4.7 13.2 - - + -
86X VAL* 2.9 35.3 + - + +
87X VAL* 3.8 7.4 - - + +
89X ALA* 1.3 74.5 - - - +
91X LYS* 1.3 62.8 + - - +
93X GLN* 4.5 3.1 - - + +
94X GLY 3.3 2.3 + - - -
95X ARG* 2.9 54.6 + - + +
96X THR* 3.0 10.6 + - - -
97X LEU* 3.8 25.8 - - + +
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Residues in contact with LYS 91 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65V ASP* 4.3 23.8 + - - +
68V GLU* 4.2 16.2 + - - -
87X VAL* 2.9 20.3 + - + +
88X TYR* 3.7 11.8 - - + +
89X ALA 3.3 0.2 - - - -
90X LEU* 1.3 75.9 - - - +
92X ARG* 1.3 63.7 + - - +
94X GLY* 3.6 8.9 + - - -
96X THR* 3.4 32.5 - - + -
98X TYR* 6.2 0.7 - - - -
102X GLY* 4.6 12.0 + - - -
76Z ARG* 5.7 6.3 - - - -
80Z TYR* 4.7 15.1 + - - +
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Residues in contact with ARG 92 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X ASP* 2.5 40.6 + - - -
72X TYR* 3.6 20.4 - - - +
88X TYR 2.9 17.0 + - - +
89X ALA 3.7 4.7 - - - +
90X LEU 3.3 0.2 - - - -
91X LYS* 1.3 79.0 - - - +
93X GLN* 1.3 83.2 + - - +
94X GLY* 3.2 1.4 + - - -
73Z GLU* 4.5 13.3 + - - +
76Z ARG* 6.3 1.6 - - - +
97Z LEU* 2.4 47.4 + - - +
98Z LEU* 4.5 8.3 + - - +
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Residues in contact with GLN 93 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61X PHE* 5.6 8.4 - - + -
64X ASN* 4.2 22.6 + - - +
65X VAL* 4.7 15.9 - - + -
68X ASP* 3.5 8.3 + - - +
89X ALA* 3.0 20.0 + - + +
90X LEU* 3.6 6.9 + - + +
91X LYS 3.4 0.2 - - - -
92X ARG* 1.3 102.4 - - - +
94X GLY* 1.3 61.1 + - - +
95X ARG* 3.5 14.9 + - + +
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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