Contacts of the helix formed by residues 52 - 66 (chain A) in PDB entry 1STU
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 VAL 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A GLY* 2.9 25.8 - - - +
48A ASN 2.8 31.9 - - - +
49A GLY* 3.4 3.6 - - - +
50A LYS 3.2 0.6 - - - +
51A LYS* 1.3 78.0 - - - +
53A SER* 1.3 58.5 + - - +
54A LYS 2.4 20.3 + - - -
55A LYS* 2.6 35.1 + - + +
56A ARG* 3.0 24.5 + - - +
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Residues in contact with SER 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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20A VAL* 4.2 6.5 - - - -
32A PHE* 2.5 48.6 + - - +
34A THR* 2.4 35.2 + - - -
45A GLY 4.2 0.3 - - - +
47A GLY* 3.8 13.0 - - - -
49A GLY 3.8 1.4 + - - -
50A LYS 3.9 11.0 - - - -
51A LYS 3.5 0.2 - - - -
52A VAL* 1.3 81.0 - - - +
54A LYS* 1.3 57.0 + - - +
57A ALA 2.9 21.3 + - - -
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Residues in contact with LYS 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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1A PRO* 5.0 3.6 - - + -
2A ILE* 3.6 37.3 - - + +
18A PHE* 5.3 7.9 - - + -
20A VAL* 4.9 16.5 - - + +
34A THR* 4.4 4.5 - - + -
50A LYS 4.9 0.6 + - - +
51A LYS 4.0 10.6 + - - +
52A VAL 2.4 11.7 + - - -
53A SER* 1.3 70.3 - - - +
55A LYS* 1.3 65.3 + - - +
57A ALA* 3.9 2.6 - - - +
58A ALA* 3.0 26.9 + - - +
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Residues in contact with LYS 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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1A PRO* 3.5 30.8 - - + +
51A LYS 4.5 1.9 + - - +
52A VAL* 2.6 30.0 + - + +
54A LYS* 1.3 76.7 - - - +
56A ARG* 1.3 60.2 + - - +
59A GLU* 3.0 55.0 + - + +
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Residues in contact with ARG 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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45A GLY* 4.4 3.1 - - - -
46A GLU 3.7 10.5 + - - +
47A GLY* 2.9 41.5 - - - +
48A ASN* 3.9 20.5 - - - +
52A VAL* 3.0 16.3 + - + +
55A LYS* 1.3 81.8 - - - +
57A ALA* 1.3 66.0 + - - +
59A GLU* 4.0 7.9 - - - +
60A LYS* 2.9 29.6 + - + +
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Residues in contact with ALA 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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18A PHE* 3.8 3.4 - - + -
34A THR* 2.8 48.7 - - + +
36A CYS* 2.8 31.1 - - - -
45A GLY* 3.9 11.3 + - - -
53A SER 2.9 9.0 + - - +
54A LYS 3.9 0.4 - - - +
56A ARG* 1.3 79.6 - - - +
58A ALA* 1.3 56.9 - - - +
60A LYS* 3.2 2.3 - - - +
61A MET 2.9 18.4 + - - -
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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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1A PRO* 3.2 32.3 - - + +
2A ILE* 4.0 0.2 - - + -
5A VAL* 3.3 4.9 - - + -
18A PHE* 3.1 32.4 - - + -
54A LYS 3.0 15.4 + - - +
57A ALA* 1.3 74.2 - - - +
59A GLU* 1.3 69.4 + - - +
61A MET* 2.6 13.7 + - - -
62A LEU* 2.8 15.0 + - + +
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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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1A PRO* 5.7 1.8 - - + -
55A LYS* 3.0 50.7 + - + +
56A ARG* 4.0 9.6 - - - +
58A ALA* 1.3 74.8 - - + +
60A LYS* 1.3 52.5 + - - +
62A LEU* 4.8 3.8 - - - +
63A VAL* 2.6 57.5 + - + +
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Residues in contact with LYS 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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43A THR* 4.3 0.2 - - - -
44A GLU 3.8 21.4 + - - +
45A GLY* 4.1 6.9 - - - -
46A GLU* 4.2 17.1 + - - +
56A ARG* 2.9 24.9 + - + +
57A ALA 3.2 5.6 - - - +
59A GLU* 1.3 78.3 - - - +
61A MET* 1.3 54.0 + - - +
63A VAL* 4.4 2.0 - - - -
64A GLU* 2.5 70.8 + - - +
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Residues in contact with MET 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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5A VAL* 3.3 18.6 - - - -
16A VAL* 4.6 0.9 - - - -
18A PHE* 4.4 0.4 - - - -
36A CYS* 2.5 44.6 - - + +
37A ILE 3.7 8.1 - - - +
38A VAL* 2.9 46.9 - - + -
43A THR* 3.5 23.3 - - - +
57A ALA 2.9 11.9 + - - +
58A ALA* 2.6 17.7 + - - +
60A LYS* 1.3 68.0 - - - +
62A LEU* 1.3 84.0 + - + +
64A GLU* 2.6 20.5 + - - +
65A LEU* 2.9 7.8 - - + +
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Residues in contact with LEU 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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1A PRO 5.2 0.2 - - - +
4A GLN* 3.8 17.5 - - + +
5A VAL* 2.8 68.2 - - + +
8A ILE* 3.5 24.2 - - + -
58A ALA 2.8 11.2 + - - +
59A GLU* 4.4 3.6 - - - +
61A MET* 1.3 72.9 - - + +
63A VAL* 1.3 66.8 + - + +
64A GLU 2.7 1.0 + - - -
65A LEU* 2.9 2.2 + - - -
66A GLN* 2.6 45.2 + - + +
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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* 2.6 50.2 + - + +
60A LYS* 4.0 3.4 - - - +
62A LEU* 1.3 75.5 - - + +
64A GLU* 1.3 69.2 + - - +
66A GLN* 4.1 4.7 - - - +
67A LYS* 3.5 47.8 + - + +
68A LEU* 5.1 0.5 - - - +
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Residues in contact with GLU 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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43A THR* 3.4 22.8 - - + +
60A LYS* 2.5 62.7 + - - +
61A MET* 2.6 23.1 + - - +
63A VAL* 1.3 81.4 - - - +
65A LEU* 1.3 63.0 + - + +
68A LEU* 3.5 27.4 - - - +
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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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8A ILE* 4.2 2.2 - - + -
14A MET* 3.2 42.0 - - + +
38A VAL* 3.8 28.3 - - + -
43A THR* 5.3 1.1 - - - +
61A MET* 2.9 19.3 - - + +
62A LEU* 2.9 13.2 + - + +
64A GLU* 1.3 81.1 - - + +
66A GLN* 1.3 77.3 + - + +
67A LYS 3.6 1.3 - - - -
68A LEU* 4.6 11.0 - - - +
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Residues in contact with GLN 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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8A ILE* 3.3 46.5 - - - +
14A MET* 5.3 0.4 - - - +
62A LEU* 2.6 49.4 + - + +
63A VAL* 4.1 2.7 - - - +
65A LEU* 1.3 82.2 - - + +
67A LYS* 1.3 67.5 + - + +
68A LEU 3.6 4.1 - - - +
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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