Contacts of the strand formed by residues 54 - 59 (chain A) in PDB entry 6PBG
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 54 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A LYS* 3.6 4.1 - - - +
27A SER* 2.8 46.0 + - - +
28A LEU 3.0 10.4 + - - +
31A GLY* 3.7 18.4 - - - +
33A ILE* 4.2 6.7 - - + -
50A HIS* 3.4 40.4 - - + +
53A PRO* 1.3 74.8 - - - +
55A ARG* 1.3 56.6 + - - +
56A GLY 3.6 15.7 - - - +
68A SER* 3.9 16.2 - - - -
69A GLY 3.5 15.7 - - - +
70A GLY* 4.6 0.2 - - - -
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Residues in contact with ARG 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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13A LYS* 3.8 47.8 - - + +
14A GLY* 3.6 19.1 - - - -
27A SER* 3.9 0.9 - - - -
29A HIS* 5.5 3.8 + - - -
53A PRO* 4.0 12.2 + - + +
54A VAL* 1.3 74.0 - - - +
56A GLY* 1.3 62.2 + - - +
57A ILE 3.8 0.7 + - - -
69A GLY 3.2 4.0 + - - -
70A GLY* 4.9 0.2 - - - -
71A ASP* 2.7 40.3 + - - +
95A TYR* 3.9 14.9 - - - -
96A ILE 3.6 14.1 + - - +
97A ARG* 3.3 58.7 - - - +
98A THR* 5.0 1.2 - - - +
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Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A VAL* 3.6 8.8 - - - +
55A ARG* 1.3 76.7 - - - +
57A ILE* 1.3 62.5 + - - +
68A SER* 3.1 5.7 - - - -
69A GLY* 3.0 28.6 + - - -
96A ILE 4.4 1.4 + - - -
97A ARG 3.9 0.8 + - - -
98A THR* 4.0 7.2 - - - -
99A THR* 3.2 31.4 - - - -
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Residues in contact with ILE 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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14A GLY* 3.3 10.8 - - - +
15A LEU* 3.2 46.9 - - - +
16A SER* 4.0 1.1 - - - +
25A LEU* 3.8 23.8 - - + +
27A SER* 3.6 14.4 - - - +
33A ILE* 3.9 26.0 - - + -
55A ARG 3.8 1.0 + - - -
56A GLY* 1.3 71.5 - - - +
58A ASP* 1.3 65.1 + - - +
66A PHE* 3.9 16.4 - - + -
67A VAL 3.3 15.7 - - - +
68A SER* 3.9 15.0 - - - -
99A THR* 3.4 7.8 + - - +
100A PHE* 4.3 8.5 - - - -
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Residues in contact with ASP 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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16A SER* 3.5 14.0 + - - -
25A LEU* 4.6 0.2 - - - -
57A ILE* 1.3 78.6 - - - +
59A PHE* 1.3 72.9 + - - +
61A LYS* 4.5 11.9 + - - -
66A PHE* 3.2 5.8 - - - -
67A VAL* 2.9 40.3 + - + +
99A THR 3.4 14.8 - - - +
100A PHE* 3.3 23.9 - - - +
101A PHE* 2.7 31.7 + - - +
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Residues in contact with PHE 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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16A SER* 2.9 40.9 + - - +
17A PHE 3.7 7.4 - - - +
18A HIS* 3.4 41.3 - + + -
19A PRO* 4.9 1.6 - - + -
23A TRP* 4.0 14.8 - + - -
25A LEU* 3.5 36.1 - - + -
35A LEU* 3.6 19.3 - - + -
58A ASP* 1.3 88.5 - - - +
60A HIS* 1.3 68.2 + - - +
61A LYS* 3.7 10.7 + - + +
65A LEU 3.7 13.5 - - - -
66A PHE* 4.0 4.9 - + + +
80A TYR* 3.7 24.9 - + + -
101A PHE* 4.0 1.9 - - - +
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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