Contacts of the helix formed by residues 74 - 90 (chain L) in PDB entry 6T9L
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 SER 74 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36L GLU* 4.5 9.7 + - - -
71L GLU 5.2 0.7 - - - -
72L MET 3.1 7.8 + - - -
73L VAL* 1.3 76.0 - - - +
75L ASP* 1.3 64.0 + - - +
76L SER* 3.0 25.4 + - - -
77L THR* 2.6 34.3 + - - +
78L ARG* 3.2 8.0 + - - +
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Residues in contact with ASP 75 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73L VAL 3.8 0.8 + - - -
74L SER* 1.3 72.1 + - - +
76L SER* 1.3 80.6 + - - +
78L ARG* 4.2 12.1 - - - +
79L GLU* 2.9 46.2 + - + +
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Residues in contact with SER 76 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L ARG* 5.7 0.3 + - - -
36L GLU* 5.0 2.1 + - - -
74L SER* 3.0 12.7 + - - -
75L ASP* 1.3 87.9 + - - +
77L THR* 1.3 67.7 + - - +
79L GLU* 4.6 2.7 - - - +
80L THR* 3.2 22.0 + - - +
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Residues in contact with THR 77 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29L LEU* 6.1 0.8 - - - +
32L ARG* 4.3 24.8 - - + +
33L LEU* 4.6 6.5 - - + -
36L GLU* 3.6 33.2 + - - +
73L VAL* 3.4 19.8 - - - +
74L SER* 2.6 29.4 + - - +
76L SER* 1.3 84.3 + - - +
78L ARG* 1.3 60.4 + - - +
80L THR* 3.2 20.1 - - - +
81L VAL* 3.3 12.8 - - - +
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Residues in contact with ARG 78 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70L LEU* 2.5 37.8 + - - +
71L GLU* 4.7 1.4 - - - +
73L VAL* 3.1 38.9 + - + +
74L SER 3.2 8.5 + - - +
75L ASP* 3.2 13.5 + - - +
77L THR* 1.3 74.7 - - - +
79L GLU* 1.3 77.0 + - - +
80L THR 3.0 3.4 + - - -
81L VAL* 3.1 21.4 - - - +
82L LEU* 3.1 21.7 + - + +
13M ASN* 6.1 0.8 - - - +
16M LEU* 4.3 21.4 - - + +
17M ASN* 5.8 1.6 + - - -
20M LEU* 4.8 11.0 - - - +
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Residues in contact with GLU 79 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75L ASP* 2.9 33.2 + - + +
76L SER* 4.8 3.1 - - - +
78L ARG* 1.3 84.4 - - - +
80L THR* 1.3 57.5 + - - +
82L LEU* 4.4 15.5 - - - +
83L LYS* 3.3 26.9 + - - +
86L ARG* 5.4 2.4 + - - -
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Residues in contact with THR 80 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32L ARG* 3.3 47.1 + - - +
76L SER 3.2 16.4 + - - +
77L THR 3.2 17.7 - - - +
79L GLU* 1.3 77.8 - - - +
81L VAL* 1.3 67.6 + - + +
83L LYS* 3.5 15.3 + - - +
84L GLN* 3.1 27.6 + - - +
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Residues in contact with VAL 81 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L ILE* 5.3 9.2 - - + +
28L GLU* 5.2 13.9 - - + +
29L LEU* 5.6 13.9 - - + -
32L ARG* 6.3 0.9 - - - -
77L THR 3.3 14.4 - - - +
78L ARG* 3.1 18.8 - - - +
80L THR* 1.3 79.1 - - + +
82L LEU* 1.3 68.9 + - + +
84L GLN* 3.2 8.2 + - + +
85L ILE* 2.9 44.1 + - + +
16M LEU* 4.5 21.5 - - + -
19M LEU* 6.4 1.3 - - + -
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Residues in contact with LEU 82 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78L ARG* 3.1 27.2 + - + +
79L GLU* 4.4 17.9 - - - +
81L VAL* 1.3 79.8 - - + +
83L LYS* 1.3 61.1 + - - +
85L ILE* 3.3 20.6 - - + +
86L ARG* 3.1 54.9 + - - +
12M SER* 4.7 8.3 - - - +
13M ASN* 4.9 15.0 - - - +
16M LEU* 3.7 33.2 - - + -
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Residues in contact with LYS 83 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L GLU 3.3 20.5 + - - +
80L THR* 3.8 15.2 + - - +
81L VAL 3.3 0.6 - - - -
82L LEU* 1.3 79.0 - - - +
84L GLN* 1.3 66.5 + - - +
86L ARG* 3.6 15.8 + - - +
87L GLU* 3.6 16.7 + - + +
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Residues in contact with GLN 84 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24L LEU* 4.8 2.4 - - - +
28L GLU* 2.9 41.0 + - - +
32L ARG* 5.4 5.2 + - - -
80L THR* 3.1 22.2 + - - +
81L VAL* 3.2 8.2 + - - +
83L LYS* 1.3 82.8 - - + +
85L ILE* 1.3 65.3 + - + +
87L GLU* 3.3 17.1 + - + +
88L PHE* 3.4 37.3 + - + -
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Residues in contact with ILE 85 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25L ILE* 4.3 28.0 - - + -
28L GLU* 5.5 0.7 - - - +
81L VAL* 2.9 26.7 + - + +
82L LEU* 3.3 30.7 - - + +
84L GLN* 1.3 75.7 - - + +
86L ARG* 1.3 55.4 + - - +
88L PHE* 2.9 9.9 + - + +
89L LEU* 2.7 47.6 + - + +
12M SER* 3.7 39.5 - - - +
15M ILE* 5.2 12.8 - - + -
16M LEU* 5.6 2.0 - - + -
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Residues in contact with ARG 86 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79L GLU* 5.4 2.4 + - - -
82L LEU* 3.1 56.3 + - - +
83L LYS* 3.6 13.8 - - - +
84L GLN 3.3 0.2 - - - -
85L ILE* 1.3 81.0 - - + +
87L GLU* 1.3 58.9 + - - +
89L LEU* 4.4 9.0 - - + +
90L GLU* 3.2 37.1 + - + +
8M ILE* 4.9 15.2 - - + +
9M ASP* 4.2 25.7 - - - +
12M SER* 4.6 10.9 + - - +
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Residues in contact with GLU 87 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83L LYS* 3.6 10.3 + - + +
84L GLN* 3.3 13.1 + - + +
85L ILE 3.2 0.4 - - - -
86L ARG* 1.3 77.4 - - - +
88L PHE* 1.3 80.3 + - + +
90L GLU* 4.5 2.6 - - - +
91L GLU* 3.2 27.0 + - - +
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Residues in contact with PHE 88 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15L TYR* 5.8 2.3 - - - -
16L LEU* 5.0 10.1 - - + +
21L ASN* 4.6 23.4 + - + +
24L LEU* 3.5 34.1 - - + -
25L ILE* 3.9 18.6 - - + -
84L GLN* 3.4 39.7 - - + -
85L ILE* 2.9 13.7 + - + +
87L GLU* 1.3 100.5 - - - +
89L LEU* 1.3 67.1 + - + +
90L GLU 3.5 0.2 - - - -
91L GLU* 3.3 32.3 - - - +
92L ILE* 5.5 1.6 - - - +
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Residues in contact with LEU 89 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L ILE* 5.5 13.9 - - + -
16L LEU* 5.8 9.0 - - + -
85L ILE* 2.7 33.7 + - + +
86L ARG* 4.4 4.9 - - + +
88L PHE* 1.3 71.7 - - + +
90L GLU* 1.3 65.3 + - - +
91L GLU 2.9 11.5 + - - -
92L ILE* 3.3 15.5 + - - +
93L VAL* 3.2 18.2 + - + +
8M ILE* 4.5 19.1 - - + +
11M ILE* 5.8 3.4 - - + -
12M SER* 4.4 26.2 - - - +
15M ILE* 4.1 22.9 - - + -
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Residues in contact with GLU 90 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86L ARG* 3.2 22.3 + - + +
87L GLU* 4.9 2.7 - - - +
89L LEU* 1.3 77.2 - - - +
91L GLU* 1.3 61.6 + - - +
92L ILE 3.1 1.5 + - - -
93L VAL* 3.5 38.2 + - - +
8M ILE* 3.4 37.0 - - + +
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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