Contacts of the helix formed by residues 71 - 79 (chain A) in PDB entry 3L8N
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 LYS 71 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU 5.3 0.9 - - - -
65A ASP 4.0 9.4 - - - +
66A SER* 3.7 23.8 + - - +
67A ALA 2.9 21.0 + - - +
68A ARG* 4.3 14.1 - - + +
69A PHE 3.5 0.2 - - - -
70A ASN* 1.3 75.2 - - - +
72A GLU* 1.3 59.4 + - + +
74A MSE 3.5 14.7 + - + +
75A TYR* 3.2 24.6 + - - +
110A ARG* 4.3 26.9 - - + +
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Residues in contact with GLU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL* 4.0 26.9 - - + +
68A ARG 3.5 19.4 + - - +
69A PHE* 3.9 8.1 - - + +
71A LYS* 1.3 77.6 - - + +
73A VAL* 1.3 56.4 + - - +
74A MSE 3.0 9.1 + - - -
75A TYR* 3.3 9.5 + - - +
76A ALA* 3.2 23.6 + - - +
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL* 4.3 15.7 - - - +
44A ILE* 5.5 5.1 - - - -
45A ALA* 4.4 7.7 - - - +
48A LEU* 4.4 14.6 - - - +
62A PHE* 4.8 7.3 - - - -
63A LEU* 4.8 1.0 - - - +
69A PHE* 3.2 12.7 + - - -
70A ASN* 3.2 15.3 + - - +
72A GLU* 1.3 79.6 - - - +
74A MSE 1.3 54.5 + - - +
76A ALA* 4.4 2.2 - - - -
77A TYR* 3.8 13.9 + - - +
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Residues in contact with MSE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 3.0 44.2 - - + +
70A ASN 3.1 9.7 + - - +
71A LYS* 3.7 12.8 - - + +
72A GLU 3.0 0.6 - - - -
73A VAL* 1.3 77.7 - - - +
75A TYR* 1.3 69.0 + - + +
76A ALA 3.3 1.3 - - - -
77A TYR* 3.2 8.7 + - + +
78A VAL* 3.1 36.2 + - - +
95A PHE* 5.1 1.8 - - + -
110A ARG* 3.3 35.2 - - + +
111A LEU* 4.3 15.9 - - + -
114A LYS* 3.4 20.6 - - + -
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Residues in contact with TYR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A LYS 3.2 14.5 + - - +
72A GLU* 3.3 11.6 + - - +
74A MSE 1.3 88.7 - - + +
76A ALA* 1.3 58.3 + - - +
78A VAL* 3.3 6.1 + - - +
79A ASP* 3.0 38.1 + - - +
114A LYS* 5.4 3.6 - - + -
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL* 3.7 33.2 - - + +
42A GLU* 4.6 7.0 - - - -
45A ALA* 4.7 4.3 - - - -
72A GLU 3.2 12.6 + - - +
73A VAL 4.9 1.3 - - - +
74A MSE 3.3 0.2 - - - -
75A TYR* 1.3 79.1 - - - +
77A TYR* 1.3 60.7 + - - +
78A VAL 3.3 0.2 - - - -
79A ASP* 3.6 13.0 + - - +
80A GLN* 3.3 27.3 - - - +
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Residues in contact with TYR 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ALA* 4.0 13.7 - - - +
48A LEU* 3.4 47.3 + - + -
49A HIS* 3.0 40.2 + + - -
59A VAL* 4.6 2.2 - - + +
63A LEU* 3.7 24.0 - - + -
73A VAL 3.8 13.7 + - - +
74A MSE 3.2 14.7 + - + +
75A TYR 3.1 0.2 - - - -
76A ALA* 1.3 80.8 - - - +
78A VAL* 1.3 62.0 + - - +
80A GLN* 3.7 13.5 + - - +
81A LEU 3.9 6.2 - - - +
95A PHE* 4.4 16.8 - + - -
98A GLY* 3.7 25.6 + - - -
99A PHE* 3.9 19.1 - + - -
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Residues in contact with VAL 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A MSE 3.1 34.0 + - - +
75A TYR* 3.3 6.7 + - - +
77A TYR* 1.3 74.1 - - + +
79A ASP* 1.3 59.8 + - - +
80A GLN 2.8 12.2 + - - -
81A LEU 3.6 18.4 + - - +
95A PHE* 3.8 26.0 - - + -
114A LYS* 3.8 16.8 - - + +
115A PHE* 4.7 8.5 - - + -
118A ARG* 3.8 29.3 - - + +
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A TYR* 3.0 23.3 + - - +
76A ALA* 3.6 9.1 + - - +
77A TYR 3.3 0.6 - - - -
78A VAL* 1.3 80.2 - - - +
80A GLN* 1.3 65.7 + - - +
118A ARG* 4.7 8.0 - - - +
121A GLU* 5.6 2.1 - - - +
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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