Contacts of the strand formed by residues 93 - 98 (chain A) in PDB entry 3E5X
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 ASN 93 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PRO* 3.6 9.1 - - - +
47A GLY* 2.7 38.1 + - - +
65A ILE* 3.4 7.0 - - - +
66A ILE* 2.8 69.7 + - - +
67A PHE 5.3 1.2 + - - -
91A GLY 3.9 1.6 + - - -
92A ASN* 1.3 72.0 - - - +
94A ILE* 1.3 61.5 + - - +
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Residues in contact with ILE 94 (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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44A ILE* 3.4 28.8 - - + +
45A MET 3.4 19.9 - - - +
48A GLU 5.2 2.6 + - - +
63A LEU* 3.7 26.5 - - + -
64A ASP 3.3 10.5 - - - +
65A ILE* 4.2 3.6 - - + -
75A LEU* 3.7 29.8 - - + -
86A LYS* 3.8 17.5 - - + +
92A ASN* 3.7 15.6 + - + +
93A ASN* 1.3 85.1 + - - +
95A TYR* 1.3 65.2 + - - +
96A ALA 4.2 0.2 - - - -
501A 3C4 3.7 28.7 - - + +
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Residues in contact with TYR 95 (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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40A GLY 5.0 2.9 + - - -
42A ALA* 4.0 15.0 - - + +
44A ILE 3.3 13.9 - - - -
46A PRO* 3.7 24.5 - - + -
62A LYS 3.8 1.7 - - - +
63A LEU* 3.6 0.3 - - - -
64A ASP* 2.7 40.6 + - + +
66A ILE* 3.4 26.2 - - + +
72A GLU* 3.4 28.3 - - - +
93A ASN 4.3 0.4 + - - -
94A ILE* 1.3 75.4 - - - +
96A ALA* 1.3 57.2 + - - +
97A THR* 3.0 32.9 + - + +
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Residues in contact with ALA 96 (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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42A ALA* 3.6 1.7 - - - -
43A VAL* 2.8 36.2 + - + -
44A ILE* 3.1 42.2 + - + +
61A ILE* 3.9 17.9 - - + -
62A LYS 3.3 5.2 - - - -
63A LEU* 4.0 13.7 - - + -
84A ILE* 4.9 0.7 - - + -
95A TYR* 1.3 74.4 - - - +
97A THR* 1.3 56.6 + - - +
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Residues in contact with THR 97 (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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40A GLY* 4.6 10.1 - - - +
41A SER 3.4 10.8 - - - +
42A ALA* 4.4 1.8 - - - -
43A VAL* 4.5 0.2 - - - -
61A ILE* 3.1 9.6 - - - -
62A LYS* 2.9 47.3 + - - +
95A TYR* 3.0 50.8 + - + +
96A ALA* 1.3 72.8 - - - +
98A ALA* 1.4 65.5 + - - +
99A MET* 3.5 4.2 + - - +
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Residues in contact with ALA 98 (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 PHE* 4.1 10.5 - - + -
38A ALA 3.4 22.7 - - - +
40A GLY* 2.7 32.2 + - - -
41A SER 2.9 12.1 + - - +
43A VAL* 4.2 4.8 - - + +
60A LYS 3.5 5.8 - - - -
61A ILE* 4.4 3.1 - - - -
97A THR* 1.4 71.1 - - - +
99A MET* 1.3 59.1 - - - +
100A GLU 3.3 14.4 - - - +
102A THR* 3.8 15.0 - - - +
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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