Contacts of the strand formed by residues 53 - 61 (chain A) in PDB entry 5A19
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 LYS 53 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASP* 2.9 33.2 + - - +
52A ALA* 1.3 72.3 - - - +
54A VAL* 1.3 59.1 + - - +
70A GLU 4.7 0.7 - - - -
71A ILE* 3.2 7.8 - - - +
72A THR* 2.7 60.6 + - + +
127A GLU* 5.4 6.3 + - - -
130A ILE* 5.9 5.4 - - - -
286A ASP* 3.4 20.4 - - - +
287A TYR* 4.6 14.1 + - - -
288A THR* 3.8 23.5 - - - +
289A LYS* 4.1 8.3 - - - +
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Residues in contact with VAL 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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41A VAL* 4.7 2.9 - - + -
42A LEU* 3.7 36.8 - - + -
45A HIS* 4.3 11.9 - - + -
52A ALA* 4.1 19.5 - - + -
53A LYS* 1.3 78.2 - - - +
55A ALA* 1.3 61.7 + - - +
56A CYS* 3.8 19.3 - - + +
70A GLU 3.9 2.7 - - - -
71A ILE* 4.0 19.3 - - + -
284A GLY 3.0 22.3 - - - +
285A LYS* 3.4 9.5 - - - -
286A ASP* 3.0 17.4 + - - +
289A LYS* 3.5 7.0 + - - -
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Residues in contact with ALA 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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54A VAL* 1.3 73.0 - - - +
56A CYS* 1.3 59.2 + - - +
57A GLU* 3.8 9.0 + - + +
69A GLY* 3.2 24.8 - - - -
70A GLU* 3.1 33.7 + - + +
71A ILE* 5.4 0.4 - - - -
284A GLY 3.3 4.0 - - - -
285A LYS* 4.9 8.3 - - + -
289A LYS* 4.1 15.9 - - - +
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Residues in contact with CYS 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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38A SER* 3.0 27.2 + - - +
41A VAL* 3.9 34.3 - - + -
54A VAL* 3.8 17.9 - - + -
55A ALA* 1.3 71.9 - - - +
57A GLU* 1.3 74.6 + - - +
58A THR* 4.3 4.3 - - - -
67A LEU* 4.3 12.1 - - - -
68A ALA 3.9 2.7 - - - -
71A ILE* 5.1 0.2 - - + -
110A LEU* 4.2 18.8 - - + -
283A SER 4.1 1.9 - - - +
284A GLY* 2.9 17.7 + - - +
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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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55A ALA* 4.6 9.0 - - - +
56A CYS* 1.3 79.6 - - - +
58A THR* 1.3 63.1 + - - +
59A VAL* 5.4 4.0 - - + +
66A LEU 3.8 0.3 - - - +
67A LEU* 3.3 4.7 - - - -
68A ALA* 2.7 50.2 + - + +
69A GLY* 5.2 1.3 - - - -
262A THR* 3.5 28.8 - - - +
283A SER 5.0 1.3 - - - +
285A LYS* 5.3 8.2 - - - -
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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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34A CYS* 3.5 28.7 + - - -
37A ILE* 3.8 9.8 - - + +
38A SER* 2.8 24.3 + - - -
56A CYS* 4.3 0.3 - - - -
57A GLU* 1.3 74.8 - - - +
59A VAL* 1.3 69.3 + - - +
65A ILE* 3.9 16.8 - - + -
66A LEU 3.3 8.3 - - - +
67A LEU* 3.4 22.3 - - + +
261A LEU* 3.5 5.0 - - - +
262A THR* 2.9 37.4 + - - -
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Residues in contact with VAL 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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34A CYS* 3.8 1.8 - - - -
57A GLU* 5.4 4.7 - - + -
58A THR* 1.3 82.5 - - - +
60A ALA* 1.3 68.1 + - - +
61A LYS* 5.7 1.3 - - + -
64A MET* 3.8 15.9 - - + +
65A ILE* 3.3 5.4 - - - -
66A LEU* 2.9 57.8 + - + +
68A ALA* 6.0 0.9 - - + -
259A ALA* 6.0 2.5 - - + -
260A GLY 3.4 3.8 - - - +
261A LEU* 3.7 26.0 - - + -
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Residues in contact with ALA 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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30A PRO* 4.4 7.6 - - + +
33A ILE* 4.8 6.1 - - + -
34A CYS* 3.5 17.0 - - - -
59A VAL* 1.3 76.7 - - - +
61A LYS* 1.3 62.0 + - - +
64A MET 3.3 8.7 - - - +
65A ILE* 4.6 9.2 - - + -
255A PRO* 4.0 22.9 - - + -
258A ASP 4.4 0.3 - - - +
259A ALA* 3.4 6.4 - - - +
260A GLY 2.9 32.9 + - - +
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Residues in contact with LYS 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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59A VAL* 5.7 1.6 - - + -
60A ALA* 1.3 76.1 - - - +
62A THR* 1.3 88.8 + - - +
63A GLY 2.9 1.7 + - - -
64A MET* 2.8 36.3 + - + +
99A PHE* 3.6 5.7 - - - -
255A PRO* 3.5 16.8 + - - +
256A GLN 3.0 26.9 + - - -
257A GLY 4.4 1.8 + - - -
258A ASP* 4.1 7.7 - - - +
259A ALA* 3.9 24.1 - - + +
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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