Contacts of the strand formed by residues 74 - 79 (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 ASP 74 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22M SER* 6.2 0.2 - - - -
23M CYS 3.6 2.7 - - - +
24M ARG* 2.7 61.2 + - - +
70M GLY* 3.1 5.2 - - - -
71M SER 3.0 27.4 + - - +
72M GLY 3.7 0.2 - - - -
73M THR* 1.3 84.9 + - - +
75M PHE* 1.3 63.3 + - - +
76M THR* 5.8 0.4 - - - -
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Residues in contact with PHE 75 (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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22M SER* 3.0 5.7 - - - -
23M CYS* 2.5 43.5 + - + -
25M ALA* 5.1 0.2 - - + -
29M VAL* 3.8 7.9 - - + -
30M SER* 4.2 0.2 - - - -
35M SER* 3.6 22.9 - - - -
37M MET* 3.3 38.1 - - + -
39M TRP* 3.7 16.6 - - + +
55M ALA* 3.8 13.5 - - + -
69M SER 3.2 8.1 - - - +
70M GLY* 3.1 16.4 - - - -
71M SER* 2.8 40.6 - - - -
72M GLY 3.4 21.3 - - - -
73M THR* 3.9 3.1 - - - -
74M ASP* 1.3 81.8 - - - +
76M THR* 1.3 63.8 + - - +
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Residues in contact with THR 76 (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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20M THR* 4.7 7.9 - - - +
21M ILE 3.1 15.0 - - - +
22M SER* 4.1 10.1 - - - -
39M TRP* 3.3 14.4 + - - -
68M GLY* 3.1 3.3 - - - -
69M SER* 2.7 50.5 + - - +
70M GLY* 6.1 0.2 - - - -
74M ASP 5.8 0.2 - - - -
75M PHE* 1.3 81.0 - - - +
77M LEU* 1.3 58.7 + - - +
78M THR* 4.5 12.8 - - - +
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Residues in contact with LEU 77 (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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19M ALA 4.0 0.3 - - - +
20M THR* 3.3 1.2 - - - -
21M ILE* 2.9 41.0 + - + +
39M TRP* 3.4 41.1 - - + -
51M LEU* 5.6 1.8 - - + -
52M ILE* 3.2 21.3 - - + -
66M PHE* 4.4 11.9 - - + -
67M SER 2.7 34.1 - - - +
68M GLY* 4.1 0.4 - - - -
76M THR* 1.3 73.0 - - - +
78M THR* 1.3 66.9 + - - +
79M ILE* 4.8 5.6 - - + -
90M TYR* 3.7 32.8 - - + -
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Residues in contact with THR 78 (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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18M ARG* 4.3 13.8 + - - +
19M ALA 3.1 15.1 + - - -
20M THR* 3.3 26.0 - - + +
65M ARG 3.0 15.9 - - - +
67M SER* 2.8 34.5 + - - +
68M GLY* 5.4 1.1 - - - -
76M THR* 4.5 10.3 - - - +
77M LEU* 1.3 83.4 - - - +
79M ILE* 1.3 66.8 + - - +
80M SER* 3.5 1.9 + - - -
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Residues in contact with ILE 79 (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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18M ARG* 3.7 2.1 - - - +
19M ALA* 3.0 27.4 + - + +
21M ILE* 6.4 0.9 - - + -
65M ARG* 3.6 28.9 - - + +
66M PHE* 3.5 30.7 - - + +
77M LEU* 4.8 6.1 - - + -
78M THR* 1.3 78.5 + - - +
80M SER* 1.3 64.9 + - - +
81M SER 3.4 10.2 + - - +
82M VAL* 4.1 9.0 - - + +
86M ASP* 3.0 40.2 - - + +
90M TYR* 3.6 18.2 - - + +
108M LEU* 3.9 17.7 - - + -
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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