Contacts of the strand formed by residues 82 - 87 (chain A) in PDB entry 5ELI
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 THR 82 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A TRP* 3.9 18.8 + - + +
63A VAL* 4.0 17.4 - - + +
64A VAL* 4.3 6.3 - - + +
77A ARG 3.6 0.2 - - - +
78A TRP* 3.1 6.5 - - - -
79A ASN 2.9 36.2 + - - -
80A GLY 3.2 0.8 - - - -
81A SER* 1.3 84.3 + - - +
83A ALA* 1.3 63.3 + - - +
95A ILE* 3.8 24.5 - - + -
96A THR 3.5 2.5 - - - +
97A LEU* 3.6 20.3 - - + +
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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
----------------------------------------------------------
64A VAL* 4.8 0.4 - - - -
76A ARG* 5.2 6.5 - - + -
77A ARG 3.0 8.7 - - - +
78A TRP* 3.5 35.6 - - + -
82A THR* 1.3 75.6 - - - +
84A ILE* 1.3 61.4 + - - +
94A THR 4.6 0.7 - - - -
95A ILE* 3.3 9.5 - - - +
96A THR* 2.9 42.8 + - - +
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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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48A LYS 4.1 5.4 - - - +
49A ALA* 4.3 3.1 - - - -
50A TRP* 4.2 8.5 - - + +
64A VAL* 3.7 33.2 - - + +
65A SER 3.8 7.2 - - - +
66A THR* 3.7 32.0 - - + +
75A LEU 3.8 2.1 - - - +
76A ARG* 3.2 5.1 - - - -
77A ARG* 2.9 55.0 + - + +
83A ALA* 1.3 76.0 - - - +
85A THR* 1.3 64.7 + - - +
93A LEU* 3.9 11.9 - - + -
94A THR 3.6 3.4 - - - -
95A ILE* 3.4 23.8 - - + -
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Residues in contact with THR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A THR* 4.6 1.3 - - - -
73A SER 4.4 4.0 - - - -
74A PHE* 3.1 24.6 + - - -
75A LEU 4.6 0.7 - - - -
76A ARG* 4.3 10.1 + - - +
84A ILE* 1.3 77.7 - - - +
86A ASP* 1.3 60.7 + - - +
92A THR 4.2 0.5 - - - +
93A LEU* 3.5 5.5 - - - +
94A THR* 2.9 59.4 + - + +
96A THR* 6.1 0.2 - - - +
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Residues in contact with ASP 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A TYR* 2.5 29.9 + - - -
46A ARG 4.5 0.9 - - - +
48A LYS* 3.3 23.9 + - - +
66A THR* 3.5 15.6 + - + +
73A SER* 3.3 24.0 + - - +
74A PHE* 3.4 24.9 + - - +
85A THR* 1.3 79.9 + - - +
87A ASP* 1.3 65.4 + - - +
88A THR* 3.1 23.7 + - - +
92A THR 3.8 1.9 - - - +
93A LEU* 3.7 10.7 - - + +
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Residues in contact with ASP 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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38A TYR* 3.5 0.3 + - - -
74A PHE* 5.9 0.4 - - - -
85A THR 4.3 0.2 - - - -
86A ASP* 1.3 71.8 + - - +
88A THR* 1.3 54.2 + - - +
89A LEU* 3.7 6.8 + - - +
90A GLY* 3.4 29.1 + - - -
91A GLY* 2.7 31.4 + - - -
92A THR* 2.9 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