Contacts of the strand formed by residues 40 - 47 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38B TYR* 3.8 16.0 + - - +
39B SER* 1.3 75.7 + - - +
41B VAL* 1.3 63.2 + - - +
57B GLU 4.5 0.7 - - - -
58B ILE* 3.3 3.6 - - - +
59B THR* 2.7 56.8 + - + +
118B GLN* 2.9 30.3 + - - +
270B ASP* 3.3 5.5 + - - +
272B SER* 3.7 31.5 + - - -
273B LYS* 4.1 8.5 - - - +
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Residues in contact with VAL 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B LEU* 3.6 34.8 - - + -
32B ILE* 3.9 43.7 - - + -
33B LEU* 5.4 0.2 - - + -
39B SER* 4.1 7.9 - - - +
40B ARG* 1.3 79.9 - - - +
42B ALA* 1.3 62.1 + - - +
43B ALA* 3.9 17.0 - - + +
57B GLU 3.6 2.9 - - - -
58B ILE* 4.4 7.4 - - + +
268B GLY 3.0 19.0 - - - +
269B LYS* 3.3 2.4 - - - -
270B ASP* 2.8 25.9 + - + +
273B LYS* 3.5 7.2 + - - +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B VAL* 1.3 72.8 - - - +
43B ALA* 1.3 60.4 + - - +
44B GLU* 3.6 10.7 + - - +
56B GLY* 3.3 8.8 - - - -
57B GLU* 2.8 49.4 + - + +
58B ILE* 5.4 0.2 - - - -
268B GLY 3.3 3.8 - - - -
269B LYS* 4.7 8.1 - - + +
273B LYS* 4.3 15.7 - - - +
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Residues in contact with ALA 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B SER* 2.7 44.8 + - - +
28B ILE* 4.1 15.0 - - + -
41B VAL* 3.9 17.5 - - + -
42B ALA* 1.3 72.3 - - - +
44B GLU* 1.3 60.4 + - - +
45B THR* 5.6 0.2 - - - +
55B ALA 3.8 4.0 - - - -
58B ILE* 5.1 0.9 - - + -
97B TYR* 4.1 16.4 - - + +
267B SER 4.0 1.6 - - - +
268B GLY* 2.7 19.0 + - - +
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 5.1 2.4 - - + +
243A CYS* 4.3 19.6 - - + +
245A LEU* 3.7 27.7 - - + +
248A ARG* 2.8 44.8 + - - -
25B SER* 3.8 0.7 - - - -
42B ALA* 4.1 12.2 - - + +
43B ALA* 1.3 74.4 - - - +
45B THR* 1.3 65.4 + - - +
53B VAL 3.8 0.3 - - - +
54B LEU* 3.5 4.0 - - - +
55B ALA* 2.7 45.7 + - + +
56B GLY* 4.6 0.2 - - - -
57B GLU* 5.8 0.4 - - - +
97B TYR* 4.9 1.0 + - - -
246B THR* 3.7 10.6 - - - +
267B SER 4.8 2.0 - - - +
269B LYS* 5.0 4.5 - - - -
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Residues in contact with THR 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A LEU* 5.1 0.7 - - - -
245A LEU* 4.4 4.7 - - - +
21B ALA* 3.5 22.6 - - - +
24B ILE* 3.7 29.2 - - + +
25B SER* 2.7 28.1 + - - -
28B ILE* 5.3 0.3 - - - +
43B ALA* 4.9 0.5 - - - +
44B GLU* 1.3 77.2 + - - +
46B LEU* 1.3 72.0 + - - +
47B CYS* 4.6 1.3 - - + +
52B VAL* 4.3 2.2 - - + -
53B VAL 3.4 8.3 - - - +
54B LEU* 3.9 8.5 - - + +
97B TYR* 5.4 0.5 + - - -
245B LEU* 3.4 4.5 - - - +
246B THR* 2.7 41.3 + - - -
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A GLU* 4.9 5.4 - - + +
46A LEU* 4.1 34.7 - - + +
53A VAL* 4.4 11.0 - - + -
55A ALA* 4.3 24.0 - - + -
245A LEU* 5.5 0.2 - - + -
45B THR* 1.3 76.7 - - - +
47B CYS* 1.3 73.1 + - - +
48B ASN* 4.6 7.0 - - + +
51B LEU* 4.9 3.6 - - + +
52B VAL* 3.4 2.4 - - - +
53B VAL* 2.7 55.1 + - + +
243B CYS* 4.1 10.8 - - - -
244B GLY 3.3 9.2 - - - +
245B LEU* 4.3 21.3 - - + -
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Residues in contact with CYS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PRO 3.7 22.9 - - - -
20B VAL* 4.0 13.5 - - + -
21B ALA* 4.0 10.3 - - - -
24B ILE* 4.9 2.9 - - + -
45B THR* 4.8 2.5 - - + -
46B LEU* 1.3 78.7 - - - +
48B ASN* 1.3 60.9 + - - +
51B LEU 3.3 7.2 - - - +
52B VAL* 4.2 15.7 - - + -
74B ILE* 6.1 1.1 - - + -
239B PRO* 3.8 26.6 - - + +
243B CYS* 3.5 4.9 - - - -
244B GLY* 2.9 40.6 + - - -
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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