Contacts of the helix formed by residues 57 - 71 (chain A) in PDB entry 1BLX
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 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56A LEU* 1.3 75.8 - - - +
58A THR* 1.3 58.5 + - - +
59A ILE 3.1 0.4 - - - -
60A ARG* 2.8 36.3 + - - +
61A GLU* 3.0 25.4 + - - +
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Residues in contact with THR 58 (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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24A TYR* 3.7 35.1 + - + -
45A VAL* 4.0 24.5 - - + -
46A ARG 4.8 0.7 + - - +
47A VAL* 4.1 17.9 - - + -
48A GLN* 5.1 3.6 + - - +
56A LEU* 2.9 4.6 + - - +
57A SER* 1.3 79.3 + - - +
59A ILE* 1.3 62.4 + - - +
61A GLU* 3.1 14.3 + - - +
62A VAL* 3.0 22.0 + - + +
166A LEU* 4.4 12.6 - - + -
169A ILE* 6.1 0.5 - - - +
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Residues in contact with ILE 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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47A VAL* 4.2 11.9 - - + +
55A PRO* 3.7 28.5 - - + -
56A LEU 3.0 12.0 + - - +
58A THR* 1.3 77.2 - - - +
60A ARG* 1.3 90.2 - - - +
62A VAL* 3.3 9.1 + - + +
63A ALA* 3.0 24.8 + - - +
92A THR* 5.8 2.9 - - + -
94A LEU* 3.8 32.8 - - + -
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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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54A MET* 4.3 21.4 - - - +
55A PRO* 3.0 26.0 + - - +
56A LEU* 4.0 6.9 + - - +
57A SER* 2.8 20.7 + - - +
59A ILE* 1.3 89.9 - - - +
61A GLU* 1.3 66.8 + - + +
62A VAL 3.2 0.2 - - - -
63A ALA* 3.3 10.3 - - + +
64A VAL* 3.1 27.6 + - + +
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Residues in contact with GLU 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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24A TYR* 4.2 2.9 + - - -
57A SER* 3.0 27.4 + - - +
58A THR* 3.5 16.4 + - - +
60A ARG* 1.3 77.4 - - + +
62A VAL* 1.3 64.1 + - - +
64A VAL* 3.3 10.4 + - + +
65A LEU* 3.1 26.2 + - - +
165A GLY 3.4 19.6 - - - +
166A LEU* 3.6 9.8 - - + +
167A ALA* 2.7 46.7 + - - +
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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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45A VAL* 4.6 6.5 - - + -
58A THR 3.0 18.3 + - - +
59A ILE* 3.5 13.2 - - + +
60A ARG 3.2 0.2 - - - -
61A GLU* 1.3 76.1 - - - +
63A ALA* 1.3 57.6 + - - +
65A LEU* 3.1 11.4 + - + +
66A ARG* 2.8 30.1 + - + +
79A LEU* 5.8 0.4 - - + -
82A VAL* 4.0 36.3 - - + -
94A LEU* 3.9 22.9 - - + -
96A LEU* 4.3 21.5 - - + -
166A LEU* 4.4 10.3 - - + -
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Residues in contact with ALA 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 ILE 3.0 13.9 + - - +
60A ARG* 3.3 16.4 - - + +
62A VAL* 1.3 78.1 - - - +
64A VAL* 1.3 52.8 + - + +
66A ARG* 3.2 9.4 + - - +
67A HIS* 2.8 34.5 + - - +
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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 3.1 15.0 + - - +
61A GLU* 3.5 12.1 - - + +
63A ALA* 1.3 73.6 - - + +
65A LEU* 1.3 61.7 + - + +
67A HIS* 3.3 10.5 + - + +
68A LEU* 2.9 36.7 + - + +
139A HIS 5.4 2.2 - - - +
141A VAL* 4.0 27.6 - - + -
165A GLY* 6.0 1.8 - - - +
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Residues in contact with LEU 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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61A GLU 3.1 21.7 + - - +
62A VAL* 3.1 10.7 + - - +
64A VAL* 1.3 77.6 - - + +
66A ARG* 1.3 63.3 + - - +
68A LEU* 3.4 11.3 + - + +
69A GLU* 3.0 23.2 + - - +
79A LEU* 4.0 15.3 - - + +
96A LEU* 4.8 11.7 - - + -
98A PHE* 4.9 15.9 - - + -
141A VAL* 6.1 0.4 - - + -
164A PHE* 3.8 40.2 - - + +
165A GLY* 4.1 9.0 - - - +
166A LEU* 3.9 33.2 - - + -
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Residues in contact with ARG 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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62A VAL* 2.8 20.1 + - + +
63A ALA* 3.2 10.5 + - - +
65A LEU* 1.3 77.1 - - - +
67A HIS* 1.3 65.2 + - - +
69A GLU* 3.1 38.8 + - - +
70A THR* 3.2 23.7 + - - +
79A LEU* 3.3 35.2 + - + +
80A PHE 4.4 2.4 + - - -
81A ASP* 4.3 15.2 + - - +
82A VAL* 3.6 19.4 - - + +
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Residues in contact with HIS 67 (chain A).
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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63A ALA 2.8 18.2 + - - +
64A VAL* 3.5 13.5 - - + +
66A ARG* 1.3 71.5 - - - +
68A LEU* 1.3 66.7 + - + +
70A THR* 2.7 36.1 + - - +
71A PHE* 3.5 34.2 - + - -
139A HIS* 4.5 12.3 + - + -
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Residues in contact with LEU 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* 2.9 26.9 + - + +
65A LEU* 3.7 14.8 - - + +
67A HIS* 1.3 77.0 - - + +
69A GLU* 1.3 62.3 + - - +
71A PHE* 3.1 25.8 + - - +
72A GLU 3.9 2.1 + - - -
73A HIS 5.0 0.7 + - - -
76A VAL* 5.9 4.6 - - + +
78A ARG* 5.7 0.3 + - - -
135A PHE* 3.7 22.5 - - + -
136A LEU* 4.1 6.1 - - + -
139A HIS* 3.6 42.6 - - + +
141A VAL* 4.1 21.1 - - + -
164A PHE* 4.0 27.4 - - + -
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Residues in contact with GLU 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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0A CA 2.4 28.6 - - - -
65A LEU 3.0 13.7 + - - +
66A ARG* 3.1 30.0 + - - +
68A LEU* 1.3 76.6 - - - +
70A THR* 1.3 58.0 - - - +
72A GLU* 3.1 20.0 + - - +
76A VAL* 5.7 1.1 - - - +
77A VAL 4.4 1.0 - - - +
78A ARG* 3.0 39.3 + - - +
79A LEU* 3.0 43.5 + - + +
80A PHE* 5.7 0.2 - - - -
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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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66A ARG* 3.2 22.4 + - - +
67A HIS* 2.7 27.5 + - - +
69A GLU* 1.3 77.0 - - - +
71A PHE* 1.3 66.6 + - - +
72A GLU* 3.5 3.6 - - - +
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Residues in contact with PHE 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 HIS* 3.5 40.2 - + - -
68A LEU* 3.1 19.4 + - - +
70A THR* 1.3 80.2 - - - +
72A GLU* 1.4 69.0 + - - +
73A HIS* 3.3 2.7 + - + +
135A PHE* 3.7 26.7 - + + -
139A HIS* 3.4 30.3 - + - -
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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