Contacts of the helix formed by residues 82 - 93 (chain P) 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 P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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-142I G 5.0 9.0 - - - -
-141I A 6.0 1.6 - - - +
85O GLN* 3.4 28.7 - - - +
88O ALA* 4.1 2.2 - - - -
78P ARG* 3.4 30.0 + - - +
80P THR* 3.1 14.6 + - + +
81P VAL* 1.3 76.9 - - - +
83P ALA* 1.3 62.7 + - - +
84P MET* 3.5 19.3 + - - +
85P ASP* 3.4 17.5 + - - +
86P VAL* 3.4 16.1 + - - +
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Residues in contact with ALA 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85O GLN* 3.0 11.4 + - - +
87O SER* 3.4 28.0 - - - +
88O ALA* 3.8 19.6 - - - +
91O ALA* 5.8 1.0 - - + +
82P THR* 1.3 72.0 - - - +
84P MET* 1.3 62.0 + - + +
85P ASP 3.3 0.2 - - - -
86P VAL* 3.3 3.8 + - - +
87P VAL* 2.9 33.0 + - - +
100P PHE* 4.4 18.6 - - + +
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Residues in contact with MET 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85O GLN* 5.9 0.2 - - - +
78P ARG* 5.5 2.2 - - - +
82P THR* 3.2 14.5 - - - +
83P ALA* 1.3 80.1 - - + +
85P ASP* 1.3 57.6 + - - +
87P VAL* 3.3 5.4 + - - +
88P TYR* 2.9 63.8 + - + +
100P PHE 3.9 14.8 - - - +
101P GLY* 3.4 26.9 - - - +
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Residues in contact with ASP 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69P ALA* 3.7 12.8 - - - +
72P TYR* 3.5 18.6 - - + +
73P THR* 2.7 34.6 + - - +
78P ARG* 2.8 39.4 + - - -
81P VAL* 4.2 3.8 - - + -
82P THR* 3.4 13.0 + - - +
83P ALA 3.3 0.6 - - - -
84P MET* 1.3 77.7 - - - +
86P VAL* 1.3 56.6 + - - +
88P TYR* 3.4 14.2 + - - +
89P ALA* 2.9 29.8 + - - +
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Residues in contact with VAL 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84O PHE* 5.3 1.8 - - + -
88O ALA* 3.7 25.8 - - + +
91O ALA* 4.4 7.2 - - + -
92O LEU* 3.8 39.3 - - + +
65P VAL* 4.8 2.5 - - + -
69P ALA* 4.3 9.4 - - + -
81P VAL* 4.4 11.9 - - + -
82P THR 3.4 15.9 - - - +
83P ALA* 3.3 9.3 + - - +
85P ASP* 1.3 73.2 - - - +
87P VAL* 1.3 62.1 + - + +
89P ALA* 3.7 1.9 - - - +
90P LEU* 2.9 42.7 + - + +
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Residues in contact with VAL 87 (chain P).
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* 5.7 2.9 - - + -
83P ALA 2.9 20.5 + - - +
84P MET 3.3 5.6 + - - +
86P VAL* 1.3 76.9 - - + +
88P TYR* 1.3 64.4 + - + +
90P LEU* 3.3 8.8 + - + +
91P LYS* 2.9 29.9 + - + +
96P THR* 5.2 6.9 - - + +
97P LEU* 4.4 20.2 - - + +
100P PHE* 3.4 36.1 - - + +
101P GLY 3.8 17.3 - - - +
102P GLY* 3.9 15.7 - - - +
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Residues in contact with TYR 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72P TYR* 3.5 36.6 + + + +
78P ARG* 6.1 0.4 - - - -
84P MET* 2.9 56.4 + - + +
85P ASP* 3.8 10.3 - - - +
87P VAL* 1.3 88.4 - - + +
89P ALA* 1.3 58.1 + - - +
91P LYS* 3.2 9.6 + - + +
92P ARG* 2.9 28.1 + - - +
101P GLY 5.0 2.0 - - - -
102P GLY 5.6 4.5 - - - -
80R TYR* 3.4 71.6 + + + +
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Residues in contact with ALA 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65P VAL* 3.3 32.5 - - + +
68P ASP* 3.7 11.8 - - + +
69P ALA* 3.5 15.5 - - + +
72P TYR* 4.2 3.7 - - - -
85P ASP 2.9 18.3 + - - +
86P VAL 3.7 4.9 - - - +
88P TYR* 1.3 75.5 - - - +
90P LEU* 1.3 56.8 + - - +
92P ARG* 3.4 2.6 + - - +
93P GLN* 3.1 33.1 + - - +
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Residues in contact with LEU 90 (chain P).
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* 4.5 2.7 - - + +
92O LEU* 5.5 2.5 - - + +
95O ALA* 3.8 25.8 - - + -
61P PHE* 3.9 24.7 - - + -
65P VAL* 3.8 23.1 - - + -
86P VAL* 2.9 33.8 + - + +
87P VAL* 3.8 6.5 - - + +
89P ALA* 1.3 74.0 - - - +
91P LYS* 1.3 63.8 + - - +
93P GLN* 4.4 2.2 - - + +
94P GLY 3.2 2.3 + - - -
95P ARG* 2.8 51.2 + - + +
96P THR* 3.3 4.2 + - - -
97P LEU* 3.8 24.9 - - + +
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Residues in contact with LYS 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65N ASP* 4.1 15.6 + - - +
68N GLU* 3.5 23.2 + - - -
72P TYR* 6.1 0.7 - - - +
87P VAL* 2.9 18.1 + - + +
88P TYR* 3.2 16.6 + - + +
90P LEU* 1.3 77.9 - - - +
92P ARG* 1.3 61.8 + - - +
94P GLY* 3.5 10.2 + - - -
96P THR* 3.3 35.3 + - + +
102P GLY 4.9 7.6 + - - -
76R ARG* 5.4 13.7 - - - +
80R TYR* 4.4 15.1 + - - +
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Residues in contact with ARG 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P ASP* 3.4 25.9 + - - +
72P TYR* 4.7 9.0 - - + +
88P TYR 2.9 16.3 + - - +
89P ALA* 3.4 6.5 + - - +
90P LEU 3.4 0.2 - - - -
91P LYS* 1.3 77.1 - - - +
93P GLN* 1.3 70.1 + - - +
94P GLY 3.5 0.5 + - - -
73R GLU* 3.9 20.9 - - - +
76R ARG* 5.8 3.4 - - - +
97R LEU* 3.0 28.6 + - + -
98R LEU* 3.3 43.8 + - + +
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Residues in contact with GLN 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61P PHE* 4.9 10.9 - - + -
64P ASN* 3.8 30.3 + - - +
65P VAL* 3.9 23.8 - - + -
68P ASP* 2.6 27.9 + - - +
89P ALA 3.1 20.5 + - - +
90P LEU* 3.6 4.5 + - - +
91P LYS 3.3 0.2 - - - -
92P ARG* 1.3 89.5 + - - +
94P GLY* 1.3 61.3 + - - +
95P ARG* 3.4 7.0 + - + +
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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