Contacts of the strand formed by residues 78 - 81 (chain A) in PDB entry 1M63
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 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A LYS* 3.6 22.0 - - - +
77A ASN* 1.3 76.8 - - - +
79A LEU* 1.3 61.4 + - - +
80A ASP* 3.8 6.6 - - - +
188A ALA* 3.7 22.9 - - + -
189A ALA 3.8 0.9 - - - +
190A LEU* 3.6 35.0 - - + +
196A LEU* 3.9 14.8 - - + -
209A LEU* 3.9 25.1 - - + +
212A ILE* 4.2 13.2 - - + -
213A ARG* 3.5 48.2 - - + +
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Residues in contact with LEU 79 (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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75A GLU* 3.5 37.2 - - + +
76A LYS* 4.5 11.4 - - + +
77A ASN 3.7 0.2 + - - -
78A LEU* 1.3 76.0 - - - +
80A ASP* 1.3 61.2 + - - +
81A ILE* 3.9 13.7 - - + -
114A LEU* 4.8 2.2 - - + -
142A LYS* 6.2 0.2 - - - +
145A PHE* 3.7 35.2 - - + -
146A LEU 4.7 3.1 - - - +
147A LEU* 4.0 24.0 - - + -
186A PRO* 4.1 20.2 - - + -
188A ALA 3.4 10.8 + - - +
189A ALA* 3.9 0.6 - - - +
190A LEU* 2.7 34.1 + - - +
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Residues in contact with ASP 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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76A LYS* 3.7 28.0 + - - +
78A LEU* 3.8 10.7 - - - +
79A LEU* 1.3 79.0 - - - +
81A ILE* 1.3 62.1 + - - +
82A ASP* 5.4 1.4 - - - +
145A PHE* 5.2 5.4 - - - -
190A LEU* 3.5 25.3 - - - +
193A GLN* 4.5 10.4 + - - -
213A ARG* 5.8 1.9 + - - -
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Residues in contact with ILE 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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79A LEU* 3.9 12.6 - - + -
80A ASP* 1.3 75.6 - - - +
82A ASP* 1.3 67.4 + - - +
85A VAL* 3.7 25.8 - - + -
112A ARG* 3.8 11.9 - - + +
113A TYR 5.4 0.4 - - - +
114A LEU* 4.2 14.1 - - + -
145A PHE* 3.7 44.0 - - + -
189A ALA* 3.6 31.6 - - + -
190A LEU 3.0 19.0 + - - +
191A MET* 4.2 5.6 - - + -
192A ASN* 2.8 28.1 + - - -
193A GLN 4.8 0.3 + - - -
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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