Contacts of the strand formed by residues 79 - 82 (chain A) in PDB entry 3MX0
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 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A HIS 3.8 4.9 - - - +
47A PRO* 4.3 6.2 - - - +
50A LYS 5.5 0.2 - - - -
51A GLY* 3.1 21.4 - - - -
52A TRP* 2.7 30.4 + - + -
69A VAL* 3.1 26.6 - - + +
71A ASN* 4.1 17.5 + - - +
77A GLN* 3.7 16.8 - - - +
78A ASP* 1.3 74.5 - - - +
80A TRP* 1.3 58.9 + - - +
182A PHE 3.4 0.5 - - - +
184A ASP* 2.8 47.7 + - + +
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Residues in contact with TRP 80 (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 LEU* 5.9 0.2 - - - -
45A THR* 4.1 0.3 - - - -
46A HIS* 3.1 40.5 + + + +
52A TRP* 2.8 19.2 - - - -
78A ASP* 2.8 36.3 + - - -
79A ASN* 1.3 70.8 - - - +
81A LEU* 1.3 56.4 + - - +
82A ARG 4.4 0.2 - - - -
122A TYR* 3.1 62.4 - + + -
134A PHE* 4.1 24.0 - + + -
136A LYS* 3.2 38.6 - - + +
139A PHE* 4.7 8.3 - + + -
181A ALA* 4.1 13.2 - - + -
182A PHE 3.0 19.5 - - - -
183A GLN* 3.4 24.3 - - + +
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Residues in contact with LEU 81 (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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43A TRP* 4.0 18.4 - - + +
44A LEU 3.7 11.2 - - - +
45A THR* 3.7 5.4 - - + +
52A TRP* 3.1 32.5 - - + +
67A TYR* 3.1 59.2 - - + -
80A TRP* 1.3 71.7 - - - +
82A ARG* 1.3 62.1 + - - +
83A THR 3.7 0.2 + - - -
181A ALA* 4.6 0.2 - - - -
182A PHE* 3.1 37.6 + - + -
191A LEU* 3.9 22.0 - - + -
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Residues in contact with ARG 82 (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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43A TRP* 3.3 13.3 - - - +
44A LEU* 2.7 41.6 + - + +
81A LEU* 1.3 71.1 - - - +
83A THR* 1.3 78.2 + - - +
84A ASN* 3.4 14.2 + - - +
129A ASP* 5.0 1.0 + - - -
130A TYR* 5.0 1.2 - - - +
131A GLY 3.2 23.4 + - - -
132A THR* 5.4 0.2 - - - +
133A ASN 3.6 21.6 + - - -
134A PHE* 3.5 35.0 - - + +
139A PHE* 3.9 9.6 - - + -
179A TYR* 3.7 31.3 + - - -
180A LEU 3.4 19.3 - - - +
181A ALA* 3.6 9.2 - - + +
131C GLY* 6.0 2.2 + - - -
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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