Contacts of the helix formed by residues 58 - 75 (chain A) in PDB entry 2LOS
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 ASP 58 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A SER 3.9 4.5 + - - -
57A GLN* 1.3 100.0 + - - +
59A PRO* 1.4 65.0 - - + +
60A ARG* 4.4 1.1 - - + +
61A ASN* 3.4 35.7 + - - +
62A VAL* 2.6 27.4 + - - +
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Residues in contact with PRO 59 (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 LEU* 5.5 7.6 - - + -
58A ASP* 1.4 81.6 - - + +
60A ARG* 1.3 67.7 + - + +
62A VAL* 2.7 24.9 - - + +
63A TRP* 3.0 16.5 + - - +
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Residues in contact with ARG 60 (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 ASP* 5.3 0.9 - - + -
59A PRO* 1.3 84.6 - - + +
61A ASN* 1.3 76.9 + - - +
63A TRP* 2.6 27.7 + - + +
64A VAL* 2.7 19.5 + - + +
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Residues in contact with ASN 61 (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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52A ALA 5.8 1.1 - - - +
57A GLN 4.2 3.4 - - - +
58A ASP* 3.4 34.5 + - + +
60A ARG* 1.3 76.4 - - - +
62A VAL* 1.3 57.2 + - + +
64A VAL* 2.6 35.5 + - - +
65A PHE* 2.9 20.5 + - + +
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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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51A GLY 3.7 20.0 - - - +
52A ALA 4.6 4.3 - - - +
54A GLN 3.6 26.7 + - - +
55A LEU* 3.9 19.1 - - + +
57A GLN 3.0 14.4 - - - +
58A ASP 2.6 28.7 - - - +
59A PRO* 2.7 30.5 - - + +
61A ASN* 1.3 76.0 - - + +
63A TRP* 1.3 51.8 - - - +
65A PHE* 2.7 32.5 + - - +
66A LEU* 2.7 23.2 + - + +
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Residues in contact with TRP 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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59A PRO 3.0 12.6 - - - +
60A ARG* 2.6 29.5 + - + +
62A VAL* 1.3 77.0 - - - +
64A VAL* 1.3 62.7 + - + -
66A LEU* 2.8 40.2 + - + +
67A ALA* 3.0 23.4 + - + +
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Residues in contact with VAL 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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60A ARG* 2.7 26.3 + - + +
61A ASN* 2.6 20.0 + - - +
63A TRP* 1.3 82.7 - - + +
65A PHE* 1.3 50.8 + - + +
67A ALA* 4.1 4.9 - - - +
68A THR* 2.5 43.7 + - - +
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Residues in contact with PHE 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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12A TRP* 6.3 2.5 - + - -
52A ALA* 3.3 21.1 - - + -
53A TYR* 3.1 46.6 - + + +
61A ASN* 2.9 19.5 + - + -
62A VAL* 2.7 16.9 + - - +
64A VAL* 1.3 71.7 - - - +
66A LEU* 1.3 59.9 + - - +
68A THR* 3.7 15.2 - - + -
69A SER* 3.0 33.9 + - - -
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Residues in contact with LEU 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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53A TYR 6.1 0.2 - - - -
54A GLN* 3.3 47.3 - - - +
55A LEU* 6.0 2.2 - - + -
62A VAL* 2.7 15.8 + - + +
63A TRP* 2.8 27.7 + - + +
65A PHE* 1.3 79.0 - - - +
67A ALA* 1.3 53.5 + - - +
69A SER* 4.7 0.7 - - - -
70A GLY* 2.7 32.7 + - - -
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Residues in contact with ALA 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 TRP* 3.0 23.3 + - + +
64A VAL* 4.1 5.2 - - - +
66A LEU* 1.3 75.3 - - - +
68A THR* 1.3 68.5 + - - +
70A GLY* 4.4 1.6 - - - -
71A THR* 3.0 25.7 + - - +
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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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64A VAL* 2.5 30.7 + - - +
65A PHE* 3.7 19.7 - - + +
67A ALA* 1.3 81.4 - - - +
69A SER* 1.3 60.9 + - - +
71A THR* 4.2 1.0 - - - -
72A LEU* 3.0 39.3 + - + +
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Residues in contact with SER 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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65A PHE* 3.0 16.0 + - - -
66A LEU 4.7 0.7 - - - -
68A THR* 1.3 79.4 - - - +
70A GLY* 1.3 58.9 + - - +
72A LEU* 4.1 8.7 - - - +
73A ALA* 2.7 46.0 + - - +
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Residues in contact with GLY 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 LEU 2.7 23.2 + - - -
67A ALA* 3.6 3.1 - - - -
68A THR 3.0 0.6 - - - -
69A SER* 1.3 78.1 - - - +
71A THR* 1.3 53.8 + - - +
73A ALA* 4.7 0.2 - - - +
74A GLY* 2.7 30.7 + - - -
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Residues in contact with THR 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 ALA* 3.0 15.2 + - - +
68A THR 4.2 0.9 - - - -
70A GLY* 1.3 73.0 - - - +
72A LEU* 1.3 71.0 + - + +
74A GLY* 4.3 1.6 - - - -
75A ILE* 2.9 30.1 + - + +
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Residues in contact with LEU 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* 3.0 29.1 + - + +
69A SER* 4.1 7.9 - - - +
71A THR* 1.3 83.4 - - + +
73A ALA* 1.3 60.7 + - - +
75A ILE* 3.2 21.4 - - - +
80A PHE* 5.0 2.9 - - - -
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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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69A SER* 2.7 30.6 + - - +
72A LEU* 1.3 70.5 - - - +
74A GLY* 1.3 52.9 + - - +
75A ILE* 3.1 2.5 - - - -
76A MET* 2.7 41.3 + - - +
79A ARG* 4.0 21.6 - - - +
80A PHE* 5.0 5.6 - - - +
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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 GLY 2.7 25.8 + - - -
71A THR* 3.0 4.4 + - - -
73A ALA* 1.3 76.6 - - - +
75A ILE* 1.3 64.7 + - - +
76A MET 2.6 12.5 - - - +
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Residues in contact with ILE 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 THR* 2.9 15.6 + - + +
72A LEU* 3.2 19.5 - - - +
74A GLY* 1.3 75.2 - - - +
76A MET* 1.3 73.4 + - + +
80A PHE* 4.3 14.4 - - + -
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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