Contacts of the strand formed by residues 40 - 49 (chain N) 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 N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9N LEU* 5.0 6.3 - - + -
19N VAL* 3.8 37.5 - - + -
31N LEU* 4.5 14.6 - - + -
33N GLY 3.8 5.6 - - - +
34N TYR* 3.9 16.2 - - + -
38N MET* 3.4 28.9 - - + +
39N ASN* 1.3 79.0 - - - +
41N VAL* 1.3 69.4 + - - +
42N LEU* 4.3 2.2 - - + -
61N VAL* 3.3 8.0 - - - +
62N ILE* 3.0 40.7 + - + -
67N VAL* 4.3 9.0 - - + -
70N VAL* 3.8 21.5 - - + -
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Residues in contact with VAL 41 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3M PRO 4.7 2.5 - - - +
4M ARG 4.3 1.3 - - - -
5M PRO* 3.4 36.6 - - + -
8M VAL* 3.9 30.1 - - + -
30N THR 3.5 0.2 - - - +
31N LEU* 3.7 4.0 - - - +
32N ASP* 2.7 49.3 + - + +
33N GLY* 3.5 16.0 + - - +
40N LEU* 1.3 81.4 - - - +
42N LEU* 1.3 59.3 + - - +
43N LEU* 4.6 9.4 - - + -
59N SER* 5.3 0.4 - - - -
60N VAL 3.2 11.7 - - - +
61N VAL* 4.2 5.4 - - + -
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Residues in contact with LEU 42 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17N VAL* 3.9 20.9 - - + -
19N VAL* 4.0 12.6 - - + -
27N PHE* 3.7 25.8 - - + -
29N GLY 4.3 6.3 - - - +
30N THR 3.2 9.0 - - - +
31N LEU* 3.8 24.9 - - + +
40N LEU* 4.9 2.5 - - + -
41N VAL* 1.3 81.8 - - - +
43N LEU* 1.3 64.5 + - - +
45N ALA* 4.3 11.1 - - + +
59N SER* 2.9 26.3 - - - -
60N VAL* 3.0 21.9 + - + +
62N ILE* 3.4 31.4 - - + -
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Residues in contact with LEU 43 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29N GLY* 3.7 0.2 - - - -
30N THR* 3.0 41.7 + - + +
32N ASP* 3.5 40.2 - - + +
41N VAL* 4.6 5.6 - - + -
42N LEU* 1.3 77.1 - - - +
44N ASP* 1.3 81.8 + - - +
45N ALA 3.4 1.0 + - - -
58N GLY 3.4 4.3 - - - +
59N SER* 3.6 21.8 - - - -
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Residues in contact with ASP 44 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N ARG 3.9 0.7 - - - +
29N GLY* 3.8 8.5 - - - -
30N THR* 4.5 3.2 + - - +
43N LEU* 1.3 84.9 - - - +
45N ALA* 1.3 59.0 + - - +
46N GLU* 5.4 1.6 - - - +
57N VAL 3.6 7.6 - - - -
58N GLY* 2.8 20.5 + - - +
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Residues in contact with ALA 45 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27N PHE* 4.2 18.6 - - + -
28N ARG 2.8 21.1 - - - +
29N GLY* 3.9 4.7 - - - -
42N LEU* 4.3 17.3 - - + -
43N LEU 4.6 0.7 - - - -
44N ASP* 1.3 75.7 - - - +
46N GLU* 1.3 68.1 + - - +
56N LYS* 3.5 4.3 - - - +
57N VAL* 3.1 37.8 + - + -
60N VAL* 4.8 1.3 - - + -
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Residues in contact with GLU 46 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26N GLU 3.8 0.7 - - - +
27N PHE* 3.1 28.5 - - - -
28N ARG* 3.0 24.1 + - + +
44N ASP 5.4 1.6 - - - +
45N ALA* 1.3 80.6 - - - +
47N GLU* 1.3 60.1 + - - +
48N ILE* 4.4 10.0 - - + +
53N VAL* 4.2 25.6 - - + +
55N ARG 3.2 10.3 - - - +
56N LYS* 2.5 41.4 + - + +
57N VAL* 5.6 0.7 - - - -
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Residues in contact with GLU 47 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20M ARG* 4.4 7.6 + - - -
69M PHE* 4.0 15.1 - - - -
25N ARG* 2.9 35.9 + - + +
26N GLU 3.9 2.2 - - - +
27N PHE* 4.2 29.8 - - + -
46N GLU* 1.3 73.0 - - - +
48N ILE* 1.3 62.7 + - - +
53N VAL* 3.2 6.8 - - - -
54N VAL* 2.8 47.2 + - + +
55N ARG* 2.8 46.0 + - + +
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Residues in contact with ILE 48 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25N ARG* 3.2 7.9 - - - +
26N GLU* 2.9 51.7 + - + +
28N ARG* 3.9 39.0 - - + +
46N GLU* 4.4 10.3 - - - +
47N GLU* 1.3 82.0 - - - +
49N GLN* 1.3 64.2 + - - +
50N ASN 5.0 0.2 - - - +
51N GLY* 3.9 32.5 - - - +
52N GLU 3.6 3.4 - - - +
53N VAL* 4.2 19.5 - - + -
54N VAL* 4.5 0.9 - - - -
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Residues in contact with GLN 49 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N GLY 5.1 2.7 - - - +
25N ARG* 2.6 48.4 + - + +
48N ILE* 1.3 75.5 - - - +
50N ASN* 1.3 64.5 + - + +
51N GLY 2.6 17.9 + - - -
52N GLU* 2.8 24.2 + - - +
54N VAL* 3.9 24.0 - - + +
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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