Contacts of the strand formed by residues 89 - 94 (chain M) in PDB entry 1I9R
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 89 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40M TYR 4.0 0.2 - - - +
41M GLN* 3.3 1.2 - - - -
42M GLN* 2.6 44.2 + - + +
88M ALA* 1.3 74.7 + - - +
90M TYR* 1.3 63.8 + - - +
91M TYR* 3.7 33.0 - - + +
105M GLY* 4.8 0.9 - - - -
106M THR 3.2 13.0 - - - +
107M LYS* 3.1 29.5 + - - +
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Residues in contact with TYR 90 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6M GLN* 2.7 29.2 + - - +
21M ILE* 3.8 25.1 - - + -
39M TRP* 5.0 5.6 - + + -
40M TYR 3.1 7.9 - - - +
41M GLN* 3.0 31.8 + - + -
51M LEU* 3.8 4.9 - - + -
66M PHE* 3.7 22.5 - + - -
77M LEU* 3.7 23.8 - - + -
79M ILE* 3.6 16.9 - - + +
86M ASP* 2.7 30.3 + - - -
88M ALA* 3.9 18.8 - - + -
89M THR* 1.3 78.4 - - - +
91M TYR* 1.3 58.7 + - - +
105M GLY* 3.3 1.3 - - - -
106M THR 2.8 22.4 + - - -
108M LEU* 4.0 11.2 - - + -
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Residues in contact with TYR 91 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39K GLN* 3.3 19.9 + - - -
44K GLY* 5.3 4.2 - - - -
45K LEU* 3.4 36.6 - - + -
6M GLN* 3.1 3.6 - - - +
39M TRP* 3.2 8.2 - - - -
40M TYR* 2.7 49.3 + - + +
42M GLN* 3.3 30.7 + - + -
48M PRO* 5.1 2.9 - - + -
89M THR* 3.7 27.2 - - + +
90M TYR* 1.3 75.0 - - - +
92M CYS* 1.3 67.0 + - - +
102M PHE* 4.4 7.9 - - + -
103M GLY 3.5 19.7 - - - -
104M GLY 3.7 9.6 - - - -
105M GLY* 3.6 19.3 - - - -
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Residues in contact with CYS 92 (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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4M LEU* 4.1 1.8 - - - -
6M GLN* 3.1 22.7 + - - -
23M CYS* 2.0 56.5 - - + -
37M MET* 4.3 4.0 - - - -
38M HIS 3.2 6.5 - - - +
39M TRP* 3.5 19.7 - - + -
91M TYR* 1.3 77.1 - - - +
93M GLN* 1.3 59.5 + - - +
102M PHE* 3.6 0.9 - - - -
103M GLY* 2.8 34.0 + - - -
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Residues in contact with GLN 93 (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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103K ASN 3.6 8.5 - - - +
105K MET* 3.5 21.0 - - - +
4M LEU* 3.7 2.0 - - - -
37M MET* 3.7 6.5 - - - -
38M HIS* 2.7 41.3 + - - -
40M TYR* 2.6 40.8 + - + -
92M CYS* 1.3 73.7 - - - +
94M HIS* 1.3 78.0 + - - +
100M PRO* 4.1 7.1 - - + +
101M THR 3.5 20.0 - - - +
102M PHE* 3.3 28.9 - - + -
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Residues in contact with HIS 94 (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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2M ILE* 3.2 51.3 - - + +
4M LEU* 3.6 10.1 - - + +
29M VAL* 4.1 10.1 - - + +
36M TYR 2.8 18.4 - - - +
37M MET* 4.1 11.4 - - + -
38M HIS* 4.2 0.2 - - - -
93M GLN* 1.3 97.3 - - - +
95M SER* 1.3 63.9 + - - +
96M TRP* 3.7 15.0 - - + +
97M GLU* 4.4 7.1 + - + -
99M PRO 3.3 13.6 + - - -
100M PRO* 3.4 7.0 - - + +
101M THR* 3.1 41.5 + - - -
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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