Contacts of the strand formed by residues 87 - 93 (chain A) in PDB entry 3PGE
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 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ASN 3.8 3.2 + - - -
26A LEU* 3.3 18.4 - - + +
27A LYS 3.1 22.9 + - - -
67A TYR* 2.8 35.5 + - + -
68A ASP* 5.1 4.3 - - - +
83A MET* 3.4 3.5 - - + -
84A GLU* 2.6 51.2 + - - +
85A ASP 3.2 2.2 - - - +
86A ASN* 1.3 81.2 - - - +
88A ILE* 1.3 61.9 + - - +
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Residues in contact with ILE 88 (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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27A LYS* 3.8 49.1 - - + +
29A SER* 4.7 4.3 - - - -
66A LEU 4.3 0.7 - - - +
67A TYR* 3.5 24.3 - - - -
68A ASP* 4.3 8.3 + - - +
86A ASN 4.1 8.7 - - - +
87A ASP* 1.3 81.5 - - - +
89A ILE* 1.3 78.7 + - - +
90A GLU* 4.5 14.6 - - + +
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Residues in contact with ILE 89 (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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26A LEU* 4.3 18.2 - - + -
27A LYS 3.3 12.4 + - - +
28A VAL* 3.4 21.0 - - + -
29A SER 3.1 23.9 + - - -
45A LEU* 5.1 8.1 - - + -
48A LEU* 5.6 1.6 - - + -
49A MET* 6.1 0.9 - - + -
65A PHE* 3.7 30.3 - - + -
66A LEU 3.7 5.6 - - - +
67A TYR* 4.4 4.9 - - + -
72A ILE* 4.3 21.1 - - + -
83A MET* 3.4 32.8 - - + -
88A ILE* 1.3 81.2 - - - +
90A GLU* 1.3 68.9 + - - +
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Residues in contact with GLU 90 (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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28A VAL* 5.7 0.2 - - - -
29A SER* 3.3 10.8 - - - +
30A ASP* 5.9 0.9 - - - -
64A ARG 3.7 0.9 - - - +
65A PHE* 3.4 5.2 - - - -
66A LEU* 3.0 49.0 + - + +
68A ASP 6.3 0.4 - - - -
88A ILE* 4.5 14.2 - - + +
89A ILE* 1.3 79.8 - - - +
91A ALA* 1.3 60.9 + - - +
92A HIS* 3.4 31.3 + - + +
101A GLU* 4.8 1.9 - - - +
134A GLU* 5.7 3.8 - - - +
135A MET 4.5 13.5 + - - +
136A ASP* 4.4 12.8 - - - +
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Residues in contact with ALA 91 (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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28A VAL* 5.2 1.6 - - + -
29A SER 2.9 10.6 + - - +
30A ASP* 3.6 21.1 - - + +
52A PHE* 3.7 33.4 - - + -
63A LEU* 4.5 10.9 - - + +
64A ARG 3.4 5.6 - - - +
65A PHE* 4.2 16.6 - - + -
90A GLU* 1.3 74.5 - - - +
92A HIS* 1.3 66.6 + - - +
93A ARG* 5.5 0.7 - - - -
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Residues in contact with HIS 92 (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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63A LEU* 3.2 9.3 - - - +
64A ARG* 2.7 52.8 + - + +
66A LEU* 3.8 33.9 - - + +
90A GLU* 3.4 31.4 + - + +
91A ALA* 1.3 81.1 + - - +
93A ARG* 1.3 93.9 + - - +
95A GLN* 4.3 4.7 - - - +
101A GLU* 4.1 8.9 + - - -
135A MET* 6.3 0.7 - - + -
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Residues in contact with ARG 93 (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 LYS* 3.7 21.1 - - - +
62A SER 4.4 1.6 - - - +
63A LEU* 4.1 7.0 - - - -
64A ARG* 4.2 0.2 - - - +
91A ALA 5.5 0.4 - - - -
92A HIS* 1.3 112.2 + - - +
94A GLU* 1.3 69.4 + - - +
95A GLN* 2.8 33.1 + - - +
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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