Contacts of the strand formed by residues 105 - 109 (chain M) in PDB entry 1N8R
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 TYR 105 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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696A C 5.1 6.6 + - - -
59M GLU* 3.7 26.9 - - + -
60M GLU 3.9 1.0 + - - -
61M ALA* 3.3 27.0 - - + +
62M ALA* 2.8 32.4 + - - -
103M ALA* 3.0 4.6 - - - -
104M ASP* 1.3 89.6 - - + +
106M VAL* 1.3 67.1 + - - +
107M LYS* 4.0 21.1 + - + +
123M ASP* 3.6 23.6 - - + +
124M ASP* 4.5 12.6 + - + -
145M LEU* 4.1 14.1 - - + -
148M GLU* 5.6 2.9 - - - -
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Residues in contact with VAL 106 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62M ALA* 3.2 10.1 - - + +
93M VAL* 3.6 36.1 - - + +
94M ARG* 3.6 27.6 - - + -
97M VAL* 3.6 16.2 - - + -
100M ALA* 4.0 27.8 - - + +
103M ALA* 5.7 0.2 - - + -
105M TYR* 1.3 75.4 - - - +
107M LYS* 1.3 63.9 + - - +
122M ALA* 4.1 1.2 - - + +
123M ASP* 2.8 23.2 + - - +
124M ASP 3.1 21.3 + - - +
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Residues in contact with LYS 107 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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696A C 4.4 17.0 + - - -
697A G 3.1 59.2 + - - +
61M ALA* 4.8 0.9 - - + -
62M ALA 2.7 13.2 + - - +
63M THR* 3.2 29.4 - - + -
64M ILE* 3.2 6.6 + - - +
105M TYR* 3.8 21.9 + - + +
106M VAL* 1.3 76.5 - - - +
108M VAL* 1.3 70.5 + - - +
109M LEU* 3.7 14.9 + - + -
124M ASP* 2.7 36.4 + - + +
125M PHE 4.4 7.9 - - - -
126M SER 4.4 0.4 - - - +
149M ARG* 5.7 0.6 - - - +
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Residues in contact with VAL 108 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64M ILE* 3.4 10.1 - - + +
66M VAL* 3.8 17.9 - - + -
69M ILE* 4.3 10.3 - - + -
93M VAL* 3.4 41.5 - - + -
107M LYS* 1.3 73.3 - - - +
109M LEU* 1.3 72.2 + - - +
120M LEU* 4.5 5.8 - - + -
122M ALA* 3.6 12.8 - - + -
124M ASP 2.8 9.3 + - - -
125M PHE* 3.5 19.1 - - + -
126M SER 3.4 23.4 + - - -
129M ALA* 3.5 9.6 - - + +
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Residues in contact with LEU 109 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688A A 4.1 14.6 - - + +
697A G 3.6 66.0 - - + +
698A A 3.7 9.4 - - - +
63M THR* 3.9 25.1 - - - +
64M ILE 2.7 12.3 + - - +
65M ASP* 3.1 17.1 - - - +
66M VAL* 2.8 30.8 + - - +
107M LYS* 3.8 17.9 - - + +
108M VAL* 1.3 74.6 - - - +
110M GLY* 1.3 59.5 - - - +
111M ALA 3.6 0.7 - - - -
126M SER* 4.0 4.0 - - - -
129M ALA* 3.8 2.9 - - - -
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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