Contacts of the strand formed by residues 40 - 47 (chain A) in PDB entry 3IML
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 ARG 40 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A TYR 4.5 10.0 + - - +
39A SER* 1.3 72.6 + - - +
41A VAL* 1.3 64.7 + - - +
57A GLU 4.6 0.7 - - - -
58A ILE* 3.2 4.6 - - - -
59A THR* 2.7 56.7 + - + +
118A GLN* 4.2 20.6 + - - +
270A ASP* 3.4 6.5 + - - +
272A SER* 3.4 36.3 + - - -
273A LYS* 4.1 9.0 - - - +
342A LYS* 5.9 4.0 - - - +
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Residues in contact with VAL 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A LEU* 3.6 34.5 - - + -
32A ILE* 4.0 42.8 - - + -
39A SER* 4.1 9.2 - - - +
40A ARG* 1.3 81.9 - - - +
42A ALA* 1.3 62.1 + - - +
43A ALA* 3.8 17.9 - - + -
57A GLU 3.7 2.7 - - - -
58A ILE* 4.3 6.5 - - + +
268A GLY 3.1 18.1 - - - +
269A LYS* 3.4 1.7 - - - -
270A ASP* 2.8 24.3 + - - +
273A LYS* 3.3 8.0 + - - +
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Residues in contact with ALA 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A VAL* 1.3 73.4 - - - +
43A ALA* 1.3 60.5 + - - +
44A GLU* 3.6 13.0 + - - +
56A GLY* 3.4 7.8 - - - -
57A GLU* 2.9 47.8 + - + +
268A GLY 3.1 5.4 - - - -
269A LYS* 4.6 8.3 - - + +
273A LYS* 4.4 14.6 - - - +
242B ASP* 6.0 0.2 - - - +
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Residues in contact with ALA 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 2.6 39.7 + - - +
28A ILE* 4.3 6.5 - - + -
41A VAL* 3.8 18.6 - - + -
42A ALA* 1.3 71.2 - - - +
44A GLU* 1.3 59.3 + - - +
45A THR* 4.9 0.2 - - - -
55A ALA 3.8 3.6 - - - -
58A ILE* 5.1 0.9 - - + -
97A TYR* 4.0 26.0 - - + +
267A SER 4.2 1.0 - - - +
268A GLY* 2.7 22.9 + - - +
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Residues in contact with GLU 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A SER* 3.8 0.7 - - - -
42A ALA* 4.0 15.5 - - - +
43A ALA* 1.3 75.1 - - - +
45A THR* 1.3 63.6 + - - +
53A VAL 3.7 0.3 - - - +
54A LEU* 3.5 4.3 - - - +
55A ALA* 2.8 46.5 + - + +
57A GLU* 5.6 1.0 - - - +
97A TYR* 4.8 0.9 + - - -
246A THR* 3.7 9.6 - - - +
267A SER 4.9 1.7 - - - +
269A LYS* 5.4 3.1 - - - +
46B LEU* 4.9 3.0 - - + +
243B CYS* 4.2 19.8 - - + +
245B LEU* 3.8 29.1 - - + +
248B ARG* 2.7 43.0 + - - -
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Residues in contact with THR 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA* 3.6 14.3 - - - +
24A ILE* 3.8 29.6 - - + +
25A SER* 2.7 30.0 + - - -
28A ILE* 5.4 0.2 - - - +
43A ALA 4.9 0.2 - - - -
44A GLU* 1.3 77.5 + - - +
46A LEU* 1.3 68.3 + - - +
47A CYS* 4.7 0.9 - - - -
52A VAL* 4.1 6.3 - - + -
53A VAL 3.2 8.5 - - - +
54A LEU* 3.7 17.0 - - + +
97A TYR* 5.3 1.2 + - - -
245A LEU* 3.3 4.2 - - - +
246A THR* 2.8 39.8 + - - -
46B LEU* 5.3 0.9 - - - -
245B LEU* 4.6 3.7 - - - +
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A THR* 1.3 75.6 - - - +
47A CYS* 1.3 68.6 + - - +
48A ASN* 4.7 5.6 - - + +
51A LEU* 5.1 3.6 - - + -
52A VAL* 3.4 2.4 - - - +
53A VAL* 2.6 59.1 + - + -
243A CYS* 4.1 15.7 - - - -
244A GLY 3.2 11.4 - - - +
245A LEU* 4.3 18.2 - - + -
44B GLU* 5.1 4.0 - - + -
46B LEU* 4.1 33.4 - - + +
53B VAL* 4.2 15.7 - - + +
55B ALA* 4.2 18.8 - - + -
245B LEU* 5.8 0.2 - - + -
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Residues in contact with CYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PRO 4.0 20.2 - - - -
20A VAL* 4.0 22.9 - - + -
21A ALA* 4.1 13.5 - - - -
24A ILE* 4.6 4.5 - - + -
45A THR* 4.7 0.4 - - - -
46A LEU* 1.3 80.1 - - - +
48A ASN* 1.3 62.0 - - - +
51A LEU 3.1 10.3 - - - +
52A VAL* 3.8 17.3 - - + -
74A ILE* 6.1 0.2 - - + -
239A PRO* 4.2 17.0 - - + +
243A CYS* 3.6 3.6 - - - -
244A GLY* 2.9 33.9 + - - +
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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