Contacts of the strand formed by residues 36 - 42 (chain B) in PDB entry 1I2M
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 36 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B GLY* 1.3 79.7 - - - +
37B VAL* 1.3 64.2 + - - +
62B LEU* 4.0 21.8 - - + -
68B ASP* 4.9 10.5 - - - +
69B VAL* 5.8 0.2 - - - -
399B ARG* 3.6 38.6 - - - +
413B LEU 3.6 0.2 - - - +
414B LEU* 3.4 3.9 - - - -
415B VAL* 2.7 46.1 + - + +
416B LYS* 5.7 0.9 - - - -
417B ASP* 4.6 15.0 - - - +
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Residues in contact with VAL 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B LEU* 1.3 75.2 - - - +
38B LEU* 1.3 68.4 + - - +
39B THR* 4.3 2.0 - - + -
62B LEU* 3.6 3.4 - - - +
63B VAL* 2.8 54.1 + - + +
65B ILE* 4.7 4.4 - - + +
69B VAL* 3.8 38.3 - - + +
72B ALA* 4.2 2.7 - - + -
81B CYS* 3.9 20.9 - - - -
91B PHE* 5.0 1.1 - - + -
412B VAL* 3.7 26.5 - - + -
413B LEU 3.5 2.9 - - - +
414B LEU* 4.1 5.2 - - + -
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Residues in contact with LEU 38 (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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37B VAL* 1.3 80.3 - - - +
39B THR* 1.3 65.8 + - - +
40B LEU* 5.4 0.2 - - - -
60B PRO* 3.7 28.5 - - + -
61B ALA 3.1 7.9 - - - +
62B LEU* 3.7 30.3 - - + +
395B GLN* 3.7 30.3 - - + +
396B LEU* 4.0 7.0 - - + -
399B ARG* 4.2 7.0 - - - +
412B VAL* 3.4 3.8 - - - +
413B LEU* 2.8 41.9 + - + +
415B VAL* 3.8 33.2 - - + -
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Residues in contact with THR 39 (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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37B VAL* 4.3 2.5 - - + -
38B LEU* 1.3 79.7 - - - +
40B LEU* 1.3 65.3 + - - +
47B GLN 4.4 0.9 - - - +
48B LEU* 2.9 48.3 + - - +
50B LEU* 4.1 5.5 - - - +
57B ARG* 4.2 1.6 - - - +
59B LYS 4.0 0.5 - - - +
61B ALA* 2.9 33.2 + - - +
63B VAL* 3.5 14.4 - - + +
91B PHE* 4.4 7.2 - - + -
410B HIS* 5.5 0.2 - - - -
411B THR 3.3 6.7 - - - -
412B VAL* 4.0 24.7 - - + -
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Residues in contact with LEU 40 (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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39B THR* 1.3 81.0 - - - +
41B GLY* 1.3 60.6 + - - +
48B LEU* 3.6 7.4 - - - -
57B ARG* 3.7 12.6 - - - +
58B LYS 4.4 2.5 - - - +
59B LYS 4.1 10.1 - - - -
60B PRO* 4.3 11.7 - - + -
375B TYR 3.6 10.8 - - - +
376B GLN 3.7 7.9 - - - +
378B GLY* 3.5 37.5 - - - +
391B MET* 3.7 18.4 - - + -
410B HIS* 3.3 4.9 - - - +
411B THR* 2.9 62.8 + - + +
413B LEU* 4.4 8.1 - - + -
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Residues in contact with GLY 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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40B LEU* 1.3 75.1 - - - +
42B GLN* 1.3 64.2 + - - -
48B LEU* 3.7 2.2 - - - +
56B GLU* 3.3 5.9 - - - +
57B ARG 2.9 36.3 + - - -
374B ASN 3.3 20.9 - - - -
375B TYR* 3.6 9.4 + - - -
376B GLN* 4.6 0.7 - - - -
409B GLN 3.6 4.9 - - - -
410B HIS* 4.2 0.2 - - - -
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Residues in contact with GLN 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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102A PRO* 6.2 0.2 - - + -
140A ARG* 5.4 4.2 + - - -
41B GLY* 1.3 77.5 - - - -
43B GLY* 1.3 58.2 + - - +
44B ASP* 3.7 14.1 - - - +
47B GLN* 3.1 23.6 + - - +
48B LEU* 3.6 4.6 - - - +
55B MET 3.6 9.1 - - - +
56B GLU* 3.0 28.9 + - - +
373B THR 4.6 1.6 + - - -
374B ASN* 3.0 38.5 + - + +
375B TYR* 3.6 6.1 - - - -
409B GLN* 2.9 43.7 + - + +
410B HIS* 3.6 7.3 - - - +
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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