Contacts of the strand formed by residues 64 - 72 (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 MET 64 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59A VAL* 4.2 27.1 - - + +
60A ALA* 3.3 6.6 - - - +
61A LYS* 2.8 50.9 + - + +
62A THR 4.0 4.7 - - - +
63A GLY* 1.3 73.0 - - - +
65A ILE* 1.3 76.0 + - - +
66A LEU* 4.0 20.6 - - + -
99A PHE* 3.9 4.1 - - - -
105A ASN* 3.5 18.8 - - + +
107A LEU* 4.1 19.1 - - + -
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Residues in contact with ILE 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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33A ILE* 5.0 2.2 - - + -
37A ILE* 3.6 11.7 - - + -
58A THR* 3.9 21.1 - - + -
59A VAL 3.3 6.1 - - - +
60A ALA* 4.6 7.4 - - + -
64A MET* 1.3 80.4 - - - +
66A LEU* 1.3 62.1 + - - +
67A LEU* 4.2 11.2 - - + -
83A VAL* 3.6 29.8 - - + -
87A VAL* 3.4 33.4 - - + -
99A PHE* 4.0 18.6 - - + -
104A CYS* 4.5 5.8 - - - -
105A ASN 2.9 13.3 + - - +
106A VAL* 3.3 5.5 - - + +
107A LEU 2.9 24.9 + - - +
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Residues in contact with LEU 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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57A GLU 3.8 0.2 - - - +
58A THR* 3.3 5.2 - - - +
59A VAL* 2.9 50.9 + - + +
64A MET* 4.0 21.0 - - + +
65A ILE* 1.3 73.8 - - - +
67A LEU* 1.3 68.5 + - - +
68A ALA* 4.2 21.8 - - + -
107A LEU* 3.3 35.9 - - + +
109A ALA* 5.0 9.4 - - + -
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Residues in contact with LEU 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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37A ILE* 3.8 17.5 - - + -
41A VAL* 4.0 8.7 - - + -
56A CYS* 4.3 7.2 - - - -
57A GLU 3.3 4.3 - - - +
58A THR* 3.4 30.7 - - + +
65A ILE* 4.2 6.3 - - + -
66A LEU* 1.3 74.3 - - - +
68A ALA* 1.3 59.4 + - - +
79A TYR* 3.8 33.9 - - + -
83A VAL* 3.8 18.2 - - + -
106A VAL* 5.4 1.8 - - + -
107A LEU 2.9 12.3 + - - +
108A VAL* 4.6 7.0 - - + -
109A ALA* 2.7 35.3 + - - +
110A LEU* 4.1 19.1 - - + -
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Residues in contact with ALA 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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56A CYS* 3.7 0.9 - - - -
57A GLU* 2.7 50.4 + - + +
59A VAL* 6.0 1.3 - - + -
66A LEU* 4.2 16.1 + - + -
67A LEU* 1.3 75.0 - - - +
69A GLY* 1.3 56.6 + - - +
109A ALA* 4.0 14.4 - - + +
110A LEU* 3.6 5.8 - - - -
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Residues in contact with GLY 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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55A ALA 3.2 12.6 - - - -
57A GLU* 5.2 2.2 - - - -
68A ALA* 1.3 76.7 - - - +
70A GLU* 1.3 76.4 + - - +
109A ALA 4.0 4.4 + - - +
110A LEU* 3.5 9.3 - - - +
111A GLU* 2.9 28.9 + - - +
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Residues in contact with GLU 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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53A LYS 4.0 1.0 - - - +
54A VAL* 3.9 1.0 - - - -
55A ALA* 3.1 46.1 + - + +
69A GLY* 1.3 85.4 - - - +
71A ILE* 1.3 63.8 + - - +
111A GLU* 3.5 19.2 - - + +
289A LYS* 5.5 0.5 + - - -
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Residues in contact with ILE 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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41A VAL* 4.5 3.1 - - + -
45A HIS* 3.5 35.0 - - + +
53A LYS 3.2 10.1 - - - +
54A VAL* 4.0 23.6 - - + -
55A ALA 4.6 0.7 - - - +
70A GLU* 1.3 81.2 - - - +
72A THR* 1.3 61.2 + - - +
73A SER* 3.6 25.4 - - - -
79A TYR* 3.7 10.8 - - - +
110A LEU* 4.0 26.7 - - + -
111A GLU 2.9 8.8 + - - +
112A GLN* 3.2 15.2 - - + +
113A GLN* 2.7 32.4 + - - +
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Residues in contact with THR 72 (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 ASP 4.3 1.4 - - - +
52A ALA* 3.4 2.6 - - - -
53A LYS* 2.7 57.5 + - + +
71A ILE* 1.3 72.0 + - - +
73A SER* 1.3 61.6 + - - +
113A GLN* 3.3 16.6 + - + +
114A SER 4.2 2.9 - - - +
115A PRO* 3.8 32.1 - - + -
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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