Contacts of the helix formed by residues 61 - 74 (chain A) in PDB entry 2LCK
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 GLY 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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58A GLN* 4.9 0.3 + - - -
59A TYR* 2.9 13.4 + - - +
60A ARG* 1.3 76.6 - - - +
62A VAL* 1.3 66.1 + - - -
63A LEU* 3.3 3.8 - - - -
64A GLY* 3.1 14.9 + - - -
65A THR* 3.4 14.4 + - - +
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Residues in contact with VAL 62 (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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37A ALA* 4.1 25.4 - - + -
60A ARG 2.7 12.5 + - - +
61A GLY* 1.3 67.6 - - - -
63A LEU* 1.3 83.1 + - + +
64A GLY 3.0 2.1 + - - -
65A THR* 3.2 23.3 + - + +
66A ILE* 3.4 8.8 - - - +
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Residues in contact with LEU 63 (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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61A GLY* 3.3 1.9 - - - -
62A VAL* 1.3 92.8 - - + +
64A GLY* 1.3 58.4 + - - +
66A ILE* 2.8 28.0 - - + +
67A LEU* 3.4 11.3 + - - +
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Residues in contact with GLY 64 (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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58A GLN* 4.1 6.1 - - - -
61A GLY* 3.1 10.2 + - - -
62A VAL 3.0 1.4 - - - -
63A LEU* 1.3 78.3 - - - +
65A THR* 1.3 63.0 + - - +
67A LEU* 3.2 14.9 + - - +
68A THR* 3.0 18.5 + - - -
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Residues in contact with THR 65 (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 THR* 4.8 16.1 + - - +
37A ALA* 5.8 2.6 + - - -
40A ARG* 5.0 11.4 - - + -
58A GLN* 3.4 34.7 - - + +
59A TYR 4.5 3.6 - - - +
60A ARG 4.8 1.6 - - - +
61A GLY 3.4 15.7 - - - +
62A VAL* 3.2 14.1 + - + +
64A GLY* 1.3 71.3 - - - +
66A ILE* 1.3 77.1 + - - +
68A THR* 3.0 20.1 + - - -
69A MET* 3.3 8.5 + - - +
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Residues in contact with ILE 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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33A PRO* 5.5 12.6 - - + -
62A VAL 3.4 10.5 - - - +
63A LEU* 2.8 38.1 - - + +
65A THR* 1.3 79.9 + - - +
67A LEU* 1.3 66.4 + - + +
69A MET* 3.2 36.4 - - - +
70A VAL* 4.1 2.8 + - - +
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Residues in contact with LEU 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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63A LEU 3.7 9.6 - - - +
64A GLY* 3.2 12.3 + - - +
65A THR 3.1 0.8 - - - -
66A ILE* 1.3 85.5 - - + +
68A THR* 1.3 61.2 + - - +
70A VAL* 3.3 27.7 - - + +
71A ARG* 3.9 11.4 + - + +
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Residues in contact with THR 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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58A GLN* 4.0 20.9 + - - +
64A GLY 3.0 14.2 + - - -
65A THR* 3.0 12.5 + - - -
67A LEU* 1.3 80.6 - - - +
69A MET* 1.3 54.1 + - - +
71A ARG* 3.5 10.4 + - - +
72A THR* 2.3 37.1 + - - +
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Residues in contact with MET 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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36A THR* 5.9 9.2 - - + -
65A THR 3.3 5.5 + - - +
66A ILE* 3.2 36.8 - - - +
68A THR* 1.3 81.7 - - - +
70A VAL* 1.3 66.8 + - + +
72A THR* 3.3 20.1 + - - -
73A GLU* 3.5 9.9 + - - +
77A SER* 4.9 3.1 + - - -
78A LEU* 3.9 26.3 - - + +
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Residues in contact with VAL 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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66A ILE 5.0 1.3 - - - +
67A LEU* 3.3 26.2 - - + +
69A MET* 1.3 84.8 - - + +
71A ARG* 1.3 66.4 + - + +
72A THR 3.1 0.4 - - - -
74A GLY* 3.0 34.8 + - - -
75A PRO* 3.8 23.4 - - + +
77A SER* 5.5 0.2 - - - -
78A LEU* 3.3 38.1 - - + -
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Residues in contact with ARG 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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67A LEU* 4.4 11.1 - - + +
68A THR* 3.5 11.7 + - - +
69A MET 3.4 0.4 - - - -
70A VAL* 1.3 85.6 - - + +
72A THR* 1.3 66.1 + - - +
73A GLU 3.5 2.3 - - - +
74A GLY* 4.6 1.6 - - - +
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Residues in contact with THR 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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68A THR* 2.3 37.1 + - - +
69A MET* 3.3 9.6 + - - -
71A ARG* 1.3 81.0 - - - +
73A GLU* 1.3 90.9 + - - +
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Residues in contact with GLU 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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69A MET* 3.5 8.2 + - - +
70A VAL 3.8 0.8 + - - -
71A ARG 4.5 2.8 - - - +
72A THR* 1.3 105.8 - - - +
74A GLY* 1.3 59.3 + - - +
77A SER* 3.2 24.8 + - - +
150A ALA* 3.9 32.5 + - + +
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Residues in contact with GLY 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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70A VAL* 3.0 18.8 + - - +
71A ARG* 5.2 0.9 - - - -
73A GLU* 1.3 79.0 - - - +
75A PRO* 1.3 68.3 - - - +
76A ARG* 3.1 7.2 - - - -
77A SER* 2.6 35.3 + - - -
78A LEU 3.9 0.9 + - - -
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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