Contacts of the helix formed by residues 65 - 76 (chain A) in PDB entry 2L53
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 PHE 65 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.9 14.4 - - + -
12A PHE 4.0 1.1 - - - -
13A LYS* 3.5 61.9 - - + -
16A PHE* 3.4 47.0 - + + -
25A GLY* 3.4 11.8 + - - +
64A ASP* 1.3 70.0 - - - +
66A PRO* 1.4 66.2 - - + +
68A PHE* 3.3 5.9 + + - +
69A LEU* 3.0 63.5 + - + +
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Residues in contact with PRO 66 (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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64A ASP* 3.6 12.1 - - + -
65A PHE* 1.4 96.9 - - + +
67A GLU* 1.3 59.0 + - + +
69A LEU* 3.5 14.0 + - + +
70A THR* 3.1 28.6 + - - -
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Residues in contact with GLU 67 (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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55A VAL* 3.8 38.7 - - + +
60A ASN* 5.5 2.1 + - - -
62A THR 4.2 3.6 - - - +
63A ILE* 3.6 17.4 - - + +
64A ASP* 2.9 45.6 + - + +
66A PRO* 1.3 75.1 - - + +
68A PHE* 1.3 64.5 + - - +
70A THR* 3.4 21.3 + - - -
71A MET* 3.8 4.9 + - - +
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Residues in contact with PHE 68 (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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12A PHE* 4.2 14.8 - - + -
16A PHE* 3.5 39.3 - + + -
27A ILE* 5.0 0.2 - - + -
32A LEU* 3.9 19.5 - - + -
35A VAL* 3.8 27.8 - - + -
36A MET* 4.1 15.7 - - + -
39A LEU* 3.9 24.2 - - + -
63A ILE* 3.6 11.7 - - + +
64A ASP 3.1 6.3 + - - +
65A PHE* 3.5 25.1 - + - +
67A GLU* 1.3 75.7 - - - +
69A LEU* 1.3 67.0 + - + +
71A MET* 3.2 27.9 + - - +
72A MET* 3.5 17.9 + - + +
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Residues in contact with LEU 69 (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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4A LEU* 3.8 24.5 - - + +
9A ILE* 3.8 26.0 - - + -
12A PHE* 4.1 19.3 - - + -
65A PHE* 3.0 62.9 + - + +
66A PRO* 3.7 12.8 - - + +
67A GLU 3.4 0.2 - - - -
68A PHE* 1.3 76.4 - - + +
70A THR* 1.3 59.2 + - - +
72A MET* 3.2 7.3 + - + +
73A ALA* 2.8 30.2 + - - +
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Residues in contact with THR 70 (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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55A VAL* 5.8 3.8 - - + -
66A PRO 3.1 15.5 + - - -
67A GLU* 3.5 14.1 + - - -
68A PHE 3.3 0.4 - - - -
69A LEU* 1.3 75.4 - - - +
71A MET* 1.3 58.5 + - + +
73A ALA* 3.4 7.5 + - + +
74A ARG* 3.0 58.7 + - + +
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Residues in contact with MET 71 (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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32A LEU* 3.8 34.5 - - + -
36A MET* 4.0 17.1 - - + +
51A MET* 3.5 60.7 - - + +
54A GLU* 6.5 0.4 - - + -
55A VAL* 3.5 29.8 - - + -
63A ILE* 4.3 3.4 - - + -
67A GLU 3.9 7.9 - - - +
68A PHE* 3.2 14.9 + - + +
70A THR* 1.3 76.3 - - + +
72A MET* 1.3 58.8 + - + +
74A ARG* 3.6 10.2 + - - +
75A LYS* 3.2 26.0 + - - +
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Residues in contact with MET 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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4A LEU* 3.8 20.0 - - + -
12A PHE* 3.5 41.1 - - + -
36A MET* 4.0 17.3 - - - -
39A LEU* 4.5 6.3 - - + -
41A GLN* 3.8 29.8 - - - +
68A PHE* 3.8 32.8 - - + +
69A LEU* 3.2 10.0 + - - +
71A MET* 1.3 73.6 - - - +
73A ALA* 1.3 63.0 + - - +
75A LYS* 3.2 17.8 + - + +
76A MET* 3.3 25.6 + - + +
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Residues in contact with ALA 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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2A ASP 3.6 19.0 - - - +
3A GLN* 3.9 9.2 - - + -
4A LEU* 3.9 29.8 - - + +
69A LEU 2.8 19.2 + - - +
70A THR* 3.4 10.1 + - + +
72A MET* 1.3 72.9 - - - +
74A ARG* 1.3 60.7 + - + +
76A MET* 3.4 14.2 + - - +
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Residues in contact with ARG 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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2A ASP 5.4 0.9 - - - -
54A GLU* 2.8 41.8 + - - +
70A THR* 3.0 42.2 + - + +
71A MET* 3.7 8.5 - - - +
72A MET 3.4 0.2 - - - -
73A ALA* 1.3 75.9 - - + +
75A LYS* 1.3 60.0 + - - +
76A MET 3.7 6.2 + - - +
77A LYS* 5.3 4.5 - - - +
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Residues in contact with LYS 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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36A MET* 6.3 1.8 - - + -
41A GLN* 3.5 27.6 - - - +
71A MET 3.2 14.7 + - - +
72A MET* 3.2 17.4 + - + +
74A ARG* 1.3 74.6 - - - +
76A MET* 1.3 71.9 + - + +
77A LYS* 3.6 6.1 + - - +
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Residues in contact with MET 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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1A ALA* 3.4 13.9 - - + +
2A ASP* 3.9 7.3 - - - +
3A GLN 4.0 17.9 - - - +
4A LEU* 3.5 31.6 - - + -
8A GLN* 4.5 19.1 - - - +
12A PHE* 5.4 1.8 - - + -
72A MET* 3.3 21.8 + - + +
73A ALA 3.4 14.9 + - - +
74A ARG 3.7 5.9 - - - +
75A LYS* 1.3 89.5 - - + +
77A LYS* 1.3 66.9 + - - +
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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