Contacts of the strand formed by residues 16 - 21 (chain M) in PDB entry 1I5L
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 PRO 16 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15M SER* 1.3 90.0 + - - +
17M VAL* 1.3 70.7 + - - +
28M ARG* 6.2 2.7 - - + -
29M GLY 3.1 12.6 - - - +
30M THR* 4.3 3.8 - - - +
72M PRO* 3.9 2.8 - - - +
73M ALA* 3.2 38.1 + - + +
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Residues in contact with VAL 17 (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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12M SER* 4.4 12.3 - - - +
15M SER* 3.9 10.8 - - - +
16M PRO* 1.3 82.5 - - - +
18M ILE* 1.3 66.6 + - - +
19M VAL* 4.1 15.0 - - + -
27M PHE 3.7 0.2 - - - +
28M ARG* 3.6 4.7 - - - +
29M GLY 2.6 40.7 + - - +
31M LEU* 4.0 22.0 - - + -
42M LEU* 4.0 22.9 - - + -
70M VAL* 4.3 12.3 - - + -
71M SER 3.4 13.5 - - - +
72M PRO* 4.4 6.7 - - + -
73M ALA* 3.7 4.8 - - - +
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Residues in contact with ILE 18 (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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17M VAL* 1.3 74.5 - - - +
19M VAL* 1.3 77.9 + - - +
20M ARG 4.3 0.7 - - - +
26M GLU* 4.7 14.8 - - + +
27M PHE 3.4 8.1 - - - +
28M ARG* 3.8 32.5 - - - +
48M ILE* 5.8 2.9 - - + -
69M PHE* 3.8 8.4 - - + +
70M VAL* 3.4 1.6 - - - +
71M SER* 2.7 40.2 + - - +
72M PRO 5.6 0.4 - - - +
73M ALA* 3.4 26.5 - - + -
55N ARG* 4.5 25.8 - - - +
57N VAL* 6.5 0.9 - - + -
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Residues in contact with VAL 19 (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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17M VAL* 4.1 11.9 - - + -
18M ILE* 1.3 86.2 - - - +
20M ARG* 1.3 63.1 + - - +
21M LEU* 3.8 25.4 + - + +
25M ARG 3.9 0.2 - - - +
26M GLU* 3.3 4.3 - - - -
27M PHE* 3.1 35.3 + - + +
40M LEU* 4.1 12.8 - - + -
42M LEU* 4.6 11.0 - - + -
62M ILE* 4.5 7.9 - - + -
67M VAL* 4.1 18.8 - - + -
69M PHE 3.4 7.9 - - - +
70M VAL* 4.0 20.2 - - + -
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Residues in contact with ARG 20 (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 ILE* 4.3 0.6 - - - +
19M VAL* 1.3 73.6 - - - +
21M LEU* 1.3 70.1 + - - +
23M GLY 4.9 2.0 - - - +
24M GLY* 3.8 29.0 + - - +
25M ARG 3.6 7.4 - - - +
26M GLU* 3.9 24.1 + - + +
67M VAL* 3.9 2.4 - - - -
68M VAL* 2.9 37.7 + - + +
69M PHE* 3.1 49.1 + - + +
25N ARG* 3.0 46.1 - - - +
47N GLU* 4.4 6.2 + - - -
55N ARG* 5.1 1.8 - - - +
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Residues in contact with LEU 21 (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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68L VAL* 3.8 16.2 - - + -
69L PHE* 5.1 2.5 - - + -
19M VAL* 4.0 13.2 - - + +
20M ARG* 1.3 82.7 + - - +
22M LYS* 1.3 63.0 + - - +
23M GLY 3.0 9.4 + - - -
24M GLY 3.1 11.8 + - - -
25M ARG* 2.8 30.2 + - + +
27M PHE* 4.2 26.0 - - + -
62M ILE* 3.7 25.8 - - + -
66M THR* 3.2 37.7 - - + +
67M VAL* 4.0 9.6 - - + -
68M VAL* 3.9 6.1 - - - +
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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