Contacts of the helix formed by residues 52 - 62 (chain A) in PDB entry 5U5S
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 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A PHE* 3.4 14.4 - - - +
30A TYR 3.1 4.1 - - - +
31A LYS 3.9 1.8 - - - -
32A PRO* 3.1 41.5 - - + +
50A PRO 5.0 1.6 - - - +
51A MET* 1.3 78.7 - - - +
53A LEU* 1.3 58.1 + - - +
54A SER* 3.0 18.4 + - - -
55A THR* 2.6 43.8 + - - -
56A VAL* 2.9 32.1 + - - +
58A ARG* 5.2 0.3 + - - -
78A MET* 4.0 6.5 - - - -
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Residues in contact with LEU 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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14A LEU* 3.4 34.9 - - + +
17A LEU* 3.7 36.3 - - + +
18A LEU* 3.7 25.8 - - + -
29A PHE* 2.9 24.8 + - + +
30A TYR* 4.8 2.2 - - + -
52A ASP* 1.3 72.1 - - - +
54A SER* 1.3 57.0 + - - +
56A VAL* 3.5 5.1 - - + +
57A LYS* 2.9 24.9 + - - +
75A VAL* 4.0 20.2 - - + -
78A MET* 3.7 28.6 - - + +
99A LEU* 4.9 4.5 - - + -
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Residues in contact with SER 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.9 8.7 - - - +
30A TYR* 2.6 21.3 + - - +
31A LYS* 3.9 12.3 - - - +
32A PRO* 5.9 0.2 - - - -
52A ASP* 3.0 13.3 + - - -
53A LEU* 1.3 79.0 - - - +
55A THR* 1.3 49.6 + - - +
57A LYS* 3.4 6.4 + - - +
58A ARG* 2.8 37.5 + - - +
61A GLU* 5.3 0.2 - - - +
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Residues in contact with THR 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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51A MET* 3.4 31.6 - - + -
52A ASP* 2.6 28.2 + - - -
54A SER* 1.3 72.8 - - - +
56A VAL* 1.3 59.9 + - - +
58A ARG* 3.3 40.9 + - - +
59A LYS* 2.8 40.3 + - + +
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Residues in contact with VAL 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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14A LEU* 3.5 18.6 - - + -
51A MET* 3.5 23.1 - - + -
52A ASP 2.9 23.2 + - - +
53A LEU* 3.5 11.4 - - + +
55A THR* 1.3 75.5 - - - +
57A LYS* 1.3 56.9 + - - +
60A MET* 2.9 26.3 + - - +
65A TYR* 3.2 27.2 + - + +
71A PHE* 3.7 22.9 - - + -
74A ASP* 4.2 15.0 - - + +
75A VAL* 4.3 9.2 - - + +
78A MET* 5.4 0.7 - - + -
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Residues in contact with LYS 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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11A ASN* 4.4 28.6 + - - +
14A LEU* 3.4 19.0 - - + +
15A LYS* 4.4 18.4 - - - +
18A LEU* 3.9 26.2 - - + +
53A LEU 2.9 16.6 + - - +
54A SER* 3.6 6.1 - - - +
56A VAL* 1.3 73.7 - - - +
58A ARG* 1.3 54.8 + - - +
60A MET* 3.1 12.3 + - + +
61A GLU* 2.6 55.8 + - + +
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Residues in contact with ARG 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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32A PRO* 6.0 2.8 - - - +
52A ASP* 5.1 1.0 + - - -
54A SER* 2.8 20.0 + - - +
55A THR* 3.2 44.4 + - - +
57A LYS* 1.3 75.4 - - - +
59A LYS* 1.3 61.0 + - - +
61A GLU* 3.1 17.3 + - - +
62A ASN* 3.0 40.9 + - - +
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Residues in contact with LYS 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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51A MET* 3.9 21.8 - - + +
55A THR* 2.8 31.6 + - + +
58A ARG* 1.3 76.9 - - + +
60A MET* 1.3 62.2 + - - +
62A ASN* 3.2 9.0 + - - +
63A ARG 3.1 3.8 + - - -
64A ASP* 3.0 34.7 + - + +
65A TYR* 3.3 24.0 - - + +
74A ASP* 3.1 26.4 + - - +
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Residues in contact with MET 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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3A LEU* 4.1 17.0 - - + +
7A LEU* 4.2 6.5 - - + +
10A CYS* 4.0 11.4 - - + -
11A ASN* 3.6 52.7 - - - +
14A LEU* 3.3 33.0 - - + -
56A VAL 2.9 14.5 + - - +
57A LYS* 3.3 11.4 - - + +
59A LYS* 1.3 77.8 - - - +
61A GLU* 1.3 56.7 + - - +
63A ARG* 2.8 33.5 + - - +
65A TYR* 3.8 22.6 - - + -
71A PHE* 4.5 3.4 - - + -
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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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11A ASN* 6.0 2.7 - - - +
54A SER 5.3 0.2 - - - +
57A LYS* 2.6 35.8 + - + +
58A ARG* 3.3 24.9 + - - +
60A MET* 1.3 71.3 - - + +
62A ASN* 1.3 64.3 + - - +
63A ARG* 3.0 30.2 + - - +
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Residues in contact with ASN 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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58A ARG* 3.0 22.3 + - - +
59A LYS* 3.6 8.3 - - - +
60A MET 3.2 0.4 - - - -
61A GLU* 1.3 80.4 + - - +
63A ARG* 1.3 70.2 + - - +
64A ASP* 3.1 22.1 + - - +
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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