Contacts of the strand formed by residues 40 - 49 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5C PRO* 4.4 0.4 - - - +
9D LEU* 4.1 19.3 - - + -
19D VAL* 3.8 28.3 - - + -
31D LEU* 4.3 15.3 - - + -
33D GLY 3.9 3.1 - - - +
34D TYR* 4.0 14.8 - - + -
38D MET* 3.4 15.9 - - + +
39D ASN* 1.3 82.2 - - - +
41D VAL* 1.3 70.1 + - - +
42D LEU* 4.2 2.7 - - + -
61D VAL* 3.4 4.3 - - - +
62D ILE* 2.9 43.6 + - + +
67D VAL* 4.1 11.0 - - + -
70D VAL* 3.8 26.7 - - + -
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Residues in contact with VAL 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3C PRO* 6.0 0.2 - - + -
4C ARG 4.2 3.1 - - - +
5C PRO* 3.3 46.0 - - + -
8C VAL* 3.8 21.8 - - + -
31D LEU* 3.6 5.9 - - - +
32D ASP* 2.7 55.3 + - + +
33D GLY 3.3 15.9 + - - +
40D LEU* 1.3 76.3 - - - +
42D LEU* 1.3 63.6 + - - +
43D LEU* 5.3 4.0 - - + -
59D SER* 5.6 0.7 - - - -
60D VAL 3.3 8.5 - - - +
61D VAL* 4.5 7.0 - - + -
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Residues in contact with LEU 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D VAL* 3.6 29.4 - - + -
19D VAL* 3.8 17.3 - - + -
27D PHE* 4.0 15.0 - - + -
29D GLY 4.3 7.0 - - - +
30D THR 3.3 14.8 - - - +
31D LEU* 3.9 11.4 - - + -
40D LEU* 5.0 2.5 - - + -
41D VAL* 1.3 78.0 - - - +
43D LEU* 1.3 63.0 + - - +
45D ALA* 4.2 12.1 - - + -
59D SER* 3.0 6.1 - - - -
60D VAL* 2.7 52.1 + - + +
62D ILE* 3.6 30.7 - - + -
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Residues in contact with LEU 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8C VAL* 6.5 0.4 - - + -
11C ARG* 5.9 5.4 - - - +
29D GLY* 3.8 0.3 - - - -
30D THR* 2.9 43.3 + - + +
32D ASP* 3.6 35.2 - - + +
41D VAL* 5.3 2.5 - - + -
42D LEU* 1.3 72.2 - - - +
44D ASP* 1.3 84.2 + - - +
45D ALA 3.4 2.0 + - - -
58D GLY 3.3 4.0 - - - +
59D SER* 3.5 25.6 - - - -
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Residues in contact with ASP 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D ARG 3.9 0.5 - - - +
29D GLY* 3.8 8.0 - - - -
30D THR* 5.9 1.3 - - - +
43D LEU* 1.3 86.8 - - - +
45D ALA* 1.3 59.1 + - - +
46D GLU* 5.3 2.1 - - - +
57D VAL 3.1 10.8 - - - -
58D GLY* 2.4 24.9 + - - +
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Residues in contact with ALA 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PHE* 4.2 10.1 - - + -
28D ARG 2.8 21.3 - - - +
29D GLY* 3.9 5.4 - - - -
42D LEU* 4.2 8.7 + - + -
43D LEU 4.6 0.4 - - - -
44D ASP* 1.3 76.6 - - - +
46D GLU* 1.3 63.3 + - - +
56D LYS* 3.3 4.9 - - - +
57D VAL* 2.8 36.2 + - + +
60D VAL* 4.1 26.2 - - + -
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Residues in contact with GLU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D PHE* 3.2 28.7 - - - -
28D ARG* 2.9 35.8 + - - +
44D ASP 5.3 1.8 - - - +
45D ALA* 1.3 79.6 - - - +
47D GLU* 1.3 62.5 + - - +
48D ILE* 3.7 9.2 + - + +
53D VAL* 3.4 30.7 - - + +
55D ARG 3.2 9.0 - - - +
56D LYS* 3.9 29.3 - - + -
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Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ARG* 3.9 22.3 + - - -
69C PHE* 3.9 28.7 - - - -
25D ARG* 4.0 19.8 - - + +
26D GLU 3.4 10.3 - - - +
27D PHE* 4.2 17.3 - - + -
46D GLU* 1.3 73.3 - - - +
48D ILE* 1.3 60.1 + - - +
49D GLN* 4.6 5.7 + - - +
53D VAL* 3.6 4.5 - - - +
54D VAL* 2.8 40.4 + - + -
55D ARG* 2.8 41.9 + - + +
57D VAL* 5.9 0.2 - - - +
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Residues in contact with ILE 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24D GLY 4.2 0.7 - - - +
25D ARG* 3.6 6.6 - - - -
26D GLU* 2.9 57.7 + - + +
28D ARG* 3.1 42.4 - - + +
46D GLU* 3.9 17.9 - - + +
47D GLU* 1.3 76.7 - - - +
49D GLN* 1.3 63.2 + - - +
50D ASN* 3.6 4.6 + - - +
51D GLY* 3.8 24.7 - - - +
52D GLU 3.5 13.5 - - - +
53D VAL* 4.9 6.5 - - + -
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Residues in contact with GLN 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ARG* 5.5 5.3 + - - +
25D ARG* 3.9 24.8 - - - +
47D GLU* 4.6 6.4 + - - +
48D ILE* 1.3 69.1 - - - +
50D ASN* 1.3 86.8 + - - +
51D GLY 2.9 2.7 + - - -
52D GLU* 3.0 42.4 + - - +
54D VAL* 3.3 30.3 - - + +
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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