Contacts of the strand formed by residues 81 - 88 (chain A) in PDB entry 4PTE
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 LEU 81 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A GLN* 3.8 21.1 - - + +
73A ALA 3.4 12.1 - - - +
74A LYS* 4.1 20.9 - - + -
79A GLY 4.6 3.6 - - - +
80A GLU* 1.3 77.3 - - - +
82A VAL* 1.3 64.5 + - - +
113A ARG* 5.6 0.7 + - - -
133A ASP* 4.2 1.9 - - - +
134A TYR* 3.2 49.9 + - + +
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Residues in contact with VAL 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A TYR* 5.5 0.2 - - + -
72A GLN* 3.3 7.8 - - - +
73A ALA* 2.8 56.1 + - + +
75A LEU* 3.8 37.7 - - + -
80A GLU 5.0 0.2 - - - -
81A LEU* 1.3 79.9 - - - +
83A ALA* 1.3 59.0 + - - +
84A ILE* 4.2 8.3 - - + -
113A ARG* 4.9 10.1 - - + +
131A VAL* 3.7 27.1 - - + -
132A LEU 3.2 15.9 - - - +
133A ASP* 4.8 2.2 - - - -
134A TYR* 3.8 5.8 - - - -
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Residues in contact with ALA 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 4.2 7.9 - - + -
70A VAL* 4.0 11.9 - - + -
71A TYR 3.2 8.7 - - - +
72A GLN* 4.5 0.7 - - - +
82A VAL* 1.3 73.2 - - - +
84A ILE* 1.3 59.9 + - - +
85A LYS 3.8 0.4 + - - -
130A LEU 3.3 2.3 - - - +
131A VAL* 3.6 0.3 - - - -
132A LEU* 2.7 45.1 + - + +
134A TYR* 4.0 3.2 - - + +
501A 2WF 3.6 38.8 - - + +
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Residues in contact with ILE 84 (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 TYR* 3.8 40.6 - - + +
59A THR* 5.8 0.7 - - + -
69A VAL 3.6 1.0 - - - +
70A VAL* 3.3 3.7 - - - -
71A TYR* 2.7 56.9 + - + +
73A ALA* 4.0 16.2 - - + -
82A VAL* 4.2 15.3 - - + -
83A ALA* 1.3 74.8 - - - +
85A LYS* 1.3 62.6 + - - +
116A PHE* 4.4 9.2 - - + -
129A ASN* 3.9 36.6 - - + +
130A LEU 3.3 5.8 - - - +
131A VAL* 4.4 10.1 - - + -
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Residues in contact with LYS 85 (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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67A PHE* 3.7 33.4 - - + +
69A VAL 3.6 3.4 - - - -
70A VAL* 4.3 11.2 - - + +
83A ALA 3.8 1.6 + - - -
84A ILE* 1.3 71.0 - - - +
86A LYS* 1.3 60.4 + - - +
87A VAL* 3.9 13.7 + - + +
97A GLU* 2.6 40.6 + - - +
128A LEU 3.5 2.3 - - - +
129A ASN* 3.4 3.1 - - - -
130A LEU* 2.8 54.2 + - + +
132A LEU* 4.7 10.1 - - + -
200A ASP* 3.3 12.9 + - - -
202A GLY* 4.3 2.4 - - - +
501A 2WF 2.9 38.5 + - + +
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Residues in contact with LYS 86 (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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67A PHE* 4.6 0.2 - - - -
68A GLY* 3.6 6.6 - - - -
69A VAL* 2.9 36.6 + - + +
71A TYR* 4.1 30.4 + - + +
84A ILE* 3.8 0.6 + - + +
85A LYS* 1.3 72.9 - - - +
87A VAL* 1.3 63.9 + - - +
118A SER* 3.8 16.2 + - - -
119A SER 3.9 8.9 + - - -
127A TYR* 3.7 45.0 - - + -
128A LEU 3.4 2.7 - - - -
129A ASN* 3.3 21.9 - - - +
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Residues in contact with VAL 87 (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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67A PHE* 3.8 24.2 - - + +
68A GLY* 5.1 0.2 - - - -
85A LYS* 3.9 32.1 - - + +
86A LYS* 1.3 78.9 - - - +
88A LEU* 1.3 69.6 + - - +
95A ASN* 4.1 17.3 - - - +
97A GLU* 4.9 6.3 - - - +
127A TYR* 3.3 8.3 - - - -
128A LEU* 2.8 54.3 + - + +
130A LEU* 5.7 4.0 - - + -
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Residues in contact with LEU 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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67A PHE 4.4 4.2 + - - -
87A VAL* 1.3 82.3 - - - +
89A GLN* 1.3 68.2 + - - +
90A ASP 3.9 1.6 + - - -
95A ASN* 4.9 3.3 + - - -
125A GLU* 4.8 14.6 - - + -
126A VAL 3.8 11.0 - - - +
127A TYR* 3.8 20.9 - - + +
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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