Contacts of the strand formed by residues 40 - 48 (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 LEU 40 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5L PRO* 4.4 0.4 - - - -
9M LEU* 4.7 9.0 - - + -
19M VAL* 4.1 17.5 - - + -
31M LEU* 4.6 12.3 - - + -
33M GLY 3.7 4.5 - - - +
34M TYR* 3.7 19.5 - - + -
38M MET* 3.4 24.5 - - + +
39M ASN* 1.3 82.4 - - - +
41M VAL* 1.3 68.9 + - - +
42M LEU* 5.3 3.1 - - + -
60M VAL 3.8 0.4 - - - +
61M VAL* 3.2 7.1 - - - +
62M ILE* 2.7 47.7 + - + -
67M VAL* 4.1 16.6 - - + -
70M VAL* 3.6 30.7 - - + -
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Residues in contact with VAL 41 (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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4L ARG 4.7 0.4 - - - +
5L PRO* 3.4 40.2 - - + -
8L VAL* 3.6 33.4 - - + -
31M LEU* 3.8 3.1 - - - +
32M ASP* 3.1 30.9 + - + +
33M GLY* 3.2 21.8 + - - +
40M LEU* 1.3 77.8 - - - +
42M LEU* 1.3 77.9 + - - +
43M LEU* 4.7 4.9 - - + -
59M SER* 5.3 0.7 - - - -
60M VAL 3.2 11.7 - - - +
61M VAL* 4.6 3.8 - - + -
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Residues in contact with LEU 42 (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* 4.0 16.6 - - + -
19M VAL* 4.6 12.1 - - + -
27M PHE* 3.9 28.7 - - + +
29M GLY* 4.2 13.5 - - - +
30M THR 3.1 22.4 - - - +
31M LEU* 3.9 11.0 - - + -
40M LEU* 5.3 3.6 - - + -
41M VAL* 1.3 84.9 - - - +
43M LEU* 1.3 65.2 + - - +
45M ALA* 4.2 7.4 - - + -
59M SER* 3.1 8.4 - - - -
60M VAL* 3.1 47.5 + - + +
62M ILE* 4.3 13.7 - - + -
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Residues in contact with LEU 43 (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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8L VAL* 6.0 1.6 - - + -
11L ARG* 5.6 6.7 - - - +
29M GLY* 4.2 0.2 - - - -
30M THR* 3.0 40.6 + - + +
32M ASP* 3.2 45.1 - - + +
41M VAL* 4.7 4.7 - - + -
42M LEU* 1.3 79.1 - - - +
44M ASP* 1.3 84.1 + - - +
45M ALA 3.5 1.1 - - - -
58M GLY 3.4 3.6 - - - +
59M SER* 3.9 16.2 - - - -
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Residues in contact with ASP 44 (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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28M ARG 4.2 0.2 - - - +
29M GLY* 4.1 6.9 - - - -
30M THR* 4.6 3.9 + - - +
43M LEU* 1.3 86.9 - - - +
45M ALA* 1.3 57.7 + - - +
46M GLU* 5.3 2.8 - - - +
57M VAL 3.8 3.8 - - - -
58M GLY* 2.6 26.6 + - - +
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Residues in contact with ALA 45 (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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27M PHE* 4.2 17.0 - - + -
28M ARG 3.1 14.8 - - - +
29M GLY* 4.2 6.5 - - - -
42M LEU* 4.2 19.3 - - + +
43M LEU 4.6 0.7 - - - -
44M ASP* 1.3 77.3 - - - +
46M GLU* 1.3 65.8 + - - +
56M LYS* 3.4 4.4 - - - +
57M VAL* 3.0 39.6 + - + +
60M VAL* 4.4 6.7 - - + -
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Residues in contact with GLU 46 (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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27M PHE* 3.2 11.0 - - - -
28M ARG* 3.0 48.9 + - + +
44M ASP 5.3 2.2 - - - +
45M ALA* 1.3 77.7 - - - +
47M GLU* 1.3 62.1 + - - +
48M ILE* 3.6 5.8 + - + +
53M VAL* 3.6 31.7 - - + +
55M ARG 3.5 10.3 - - - +
56M LYS* 2.4 42.5 + - + +
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Residues in contact with GLU 47 (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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20L ARG* 3.5 4.4 + - - -
69L PHE* 4.8 7.0 - - - -
25M ARG* 3.0 34.3 + - + -
26M GLU 3.5 7.4 - - - +
27M PHE* 4.5 26.1 - - + +
46M GLU* 1.3 71.0 - - - +
48M ILE* 1.3 63.7 + - - +
54M VAL* 3.1 32.9 + - + +
55M ARG* 2.8 60.7 + - + +
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Residues in contact with ILE 48 (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* 5.8 3.1 - - + -
24M GLY 5.0 1.2 - - - +
25M ARG* 4.7 4.7 - - - +
26M GLU* 2.6 51.8 + - + +
27M PHE 5.1 1.6 - - - -
28M ARG* 3.6 48.0 - - + +
46M GLU* 4.1 15.0 - - + +
47M GLU* 1.3 78.3 - - - +
49M GLN* 1.3 87.4 + - - +
50M ASN 4.0 0.7 - - - +
51M GLY* 3.6 11.0 - - - +
52M GLU 3.4 34.3 - - - +
53M VAL* 5.0 4.7 - - + +
54M VAL* 4.6 1.8 - - - -
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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