Contacts of the helix formed by residues 48 - 69 (chain A) in PDB entry 1SX9
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 GLU 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A LEU 3.6 9.2 + - - +
47A ASN* 1.3 75.2 - - - +
49A SER* 1.3 67.5 + - - +
51A LYS* 3.1 32.7 + - - +
52A ARG* 3.4 36.9 + - - +
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Residues in contact with SER 49 (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 ASN* 3.1 3.6 - - - +
48A GLU* 1.3 79.9 + - - +
50A GLU* 1.3 73.3 + - - +
52A ARG* 4.2 15.2 + - - +
53A PRO* 3.1 26.7 - - - +
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Residues in contact with GLU 50 (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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15A TRP* 4.3 23.3 - - + +
19A ALA* 5.7 8.3 - - + -
42A LEU* 5.7 2.8 - - - +
47A ASN* 2.7 37.0 + - - +
49A SER* 1.3 93.6 - - - +
51A LYS* 1.3 55.0 + - + +
53A PRO* 3.3 9.0 - - - +
54A PHE* 2.7 30.5 + - + -
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Residues in contact with LYS 51 (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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15A TRP* 5.1 3.8 - - + +
46A LEU* 3.1 46.2 - - + -
47A ASN 3.2 7.9 - - - +
48A GLU* 3.1 38.5 + - - +
50A GLU* 1.3 77.0 - - + +
52A ARG* 1.3 67.1 + - - +
54A PHE* 3.3 11.0 - - + -
55A VAL* 2.8 34.7 + - + +
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Residues in contact with ARG 52 (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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48A GLU* 3.4 32.7 + - - +
49A SER* 4.2 17.3 + - - +
51A LYS* 1.3 76.4 - - - +
53A PRO* 1.3 90.8 - - + +
55A VAL* 3.1 20.0 - - - +
56A GLU* 3.4 19.9 - - + +
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Residues in contact with PRO 53 (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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49A SER 3.1 24.7 - - - +
50A GLU* 3.3 8.5 - - - +
52A ARG* 1.3 109.2 - - + +
54A PHE* 1.3 61.4 + - + +
56A GLU* 3.9 19.0 + - - +
57A GLU* 4.5 2.3 + - - +
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Residues in contact with PHE 54 (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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11A ALA* 3.9 26.5 - - + -
14A VAL* 3.5 32.3 - - + -
15A TRP* 3.0 44.9 - + - -
50A GLU* 2.7 30.7 - - + -
51A LYS* 3.3 17.0 - - - -
53A PRO* 1.3 77.0 - - + +
55A VAL* 1.3 82.7 + - + +
56A GLU 3.2 0.9 - - - -
57A GLU* 3.1 12.5 + - - +
58A ALA* 3.1 24.3 + - + +
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Residues in contact with VAL 55 (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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11A ALA* 6.3 0.4 - - + -
15A TRP* 5.8 0.4 - - + -
51A LYS* 2.8 35.2 - - + +
52A ARG* 3.1 15.7 - - - +
54A PHE* 1.3 104.9 - - + +
56A GLU* 1.3 68.9 + - + +
58A ALA* 3.1 7.7 + - + +
59A GLU* 3.0 32.1 + - + +
62A ARG* 4.2 2.1 + - - +
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Residues in contact with GLU 56 (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 ARG* 3.4 27.0 - - + +
53A PRO* 3.9 10.5 - - - +
54A PHE 3.2 0.6 - - - -
55A VAL* 1.3 82.1 - - + +
57A GLU* 1.3 61.4 + - - +
59A GLU* 3.2 23.0 - - - +
60A ARG* 3.2 30.3 + - - +
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Residues in contact with GLU 57 (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 PRO 4.5 2.3 + - - +
54A PHE* 3.1 13.3 + - - +
56A GLU* 1.3 76.5 - - - +
58A ALA* 1.3 62.5 + - - +
59A GLU 3.0 1.0 + - - -
60A ARG* 3.0 18.6 + - + +
61A LEU* 2.7 43.1 - - + +
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Residues in contact with ALA 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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11A ALA* 5.2 8.5 - - + -
14A VAL* 5.6 4.5 - - + -
54A PHE* 3.1 21.3 + - + +
55A VAL* 3.1 12.3 + - + +
57A GLU* 1.3 77.2 + - - +
59A GLU* 1.3 65.5 + - - +
61A LEU* 3.3 10.3 + - - +
62A ARG* 3.1 45.8 + - - +
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Residues in contact with GLU 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 VAL* 3.0 16.1 + - + +
56A GLU* 3.2 32.2 + - - +
57A GLU 3.0 0.2 + - - -
58A ALA* 1.3 78.6 - - - +
60A ARG* 1.3 79.2 + - - +
62A ARG* 3.2 20.6 + - - +
63A VAL* 3.3 19.3 + - - +
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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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56A GLU* 3.2 29.6 + - - +
57A GLU* 3.0 11.6 + - + +
59A GLU* 1.3 86.9 + - - +
61A LEU* 1.3 69.4 + - + +
63A VAL* 2.7 31.8 + - + +
64A GLN* 3.0 23.2 + - + +
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Residues in contact with LEU 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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8A PRO* 4.5 22.2 - - + -
57A GLU* 2.7 56.5 + - + +
58A ALA* 3.8 9.4 - - - +
59A GLU 3.3 0.4 - - - -
60A ARG* 1.3 80.4 - - + +
62A ARG* 1.3 64.9 + - - +
64A GLN* 4.0 12.2 - - - +
65A HIS* 3.4 41.9 + - + +
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Residues in contact with ARG 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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8A PRO* 5.3 5.1 - - + +
11A ALA* 4.1 22.6 - - - +
55A VAL* 4.2 3.0 + - - +
58A ALA* 3.1 44.8 + - - +
59A GLU* 3.2 20.9 + - - +
60A ARG 3.2 0.4 - - - -
61A LEU* 1.3 79.9 - - + +
63A VAL* 1.3 57.0 + - - +
65A HIS* 4.3 1.6 - - - +
66A LYS* 2.9 36.0 + - + +
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Residues in contact with VAL 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 GLU 3.3 6.7 + - - +
60A ARG* 2.7 37.5 + - + +
62A ARG* 1.3 80.0 - - - +
64A GLN* 1.3 71.1 + - + +
66A LYS* 3.7 14.4 - - - +
67A LYS* 3.0 26.5 + - + +
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Residues in contact with GLN 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* 3.0 31.1 + - + +
61A LEU* 4.0 15.3 - - - +
63A VAL* 1.3 87.6 - - + +
65A HIS* 1.3 73.8 + - + +
67A LYS* 2.7 35.2 - - + +
68A ASP* 3.4 2.3 + - - +
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Residues in contact with HIS 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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6A LYS* 4.4 35.6 + - + +
8A PRO* 3.1 44.3 - - + +
61A LEU* 3.4 25.3 + - + +
62A ARG* 4.3 1.6 - - - +
64A GLN* 1.3 91.1 + - + +
66A LYS* 1.3 62.9 + - - +
68A ASP* 3.1 13.3 + - - +
69A HIS* 2.8 37.2 + - + +
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Residues in contact with LYS 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 ARG* 2.9 23.2 + - + +
63A VAL* 3.7 14.3 - - - +
65A HIS* 1.3 77.1 - - - +
67A LYS* 1.3 78.5 + - - +
69A HIS* 3.1 7.3 + - - +
70A PRO* 2.9 40.3 - - + +
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Residues in contact with LYS 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 VAL* 3.0 21.0 + - + +
64A GLN* 2.7 25.6 - - - +
66A LYS* 1.3 92.8 - - - +
68A ASP* 1.3 82.6 + - + +
70A PRO* 2.8 18.8 - - - +
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Residues in contact with ASP 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 GLN 4.1 6.3 - - - +
65A HIS* 3.1 12.2 + - - +
67A LYS* 1.3 90.5 - - + +
69A HIS* 1.3 78.2 + - + +
70A PRO* 3.0 7.1 - - - +
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Residues in contact with HIS 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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5A VAL* 4.1 32.6 - - + +
6A LYS* 4.3 28.7 + - + +
65A HIS* 2.8 36.7 + - + +
66A LYS* 3.1 5.6 + - - +
68A ASP* 1.3 95.8 + - + +
70A PRO* 1.3 65.2 - - - +
71A ASP 3.3 1.8 - - - -
72A TYR* 2.8 36.0 + - + +
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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