Contacts of the helix formed by residues 34 - 41 (chain A) in PDB entry 3IIL
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 VAL 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ILE* 4.7 2.2 - - + +
33A ASN* 1.3 71.2 - - - +
35A GLY* 1.3 59.5 + - - +
37A LEU* 3.2 7.2 + - + +
38A ALA* 2.9 29.0 + - - +
56A LEU* 4.3 12.3 - - + -
61A VAL* 4.1 23.8 - - + -
65A LEU* 4.5 13.7 - - + -
76A VAL* 3.5 31.0 - - + -
77A ASP 3.0 16.3 + - - +
78A TYR* 3.6 30.7 - - + -
84A PHE* 4.1 10.8 - - + -
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Residues in contact with GLY 35 (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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33A ASN* 3.2 6.7 + - - -
34A VAL* 1.3 79.6 - - - +
36A ASP* 1.3 62.0 + - - +
38A ALA* 3.4 6.5 + - - +
39A ARG* 3.1 36.2 + - - +
44A TYR* 4.2 1.2 + - - -
56A LEU* 5.8 0.9 - - - -
77A ASP 4.6 0.2 + - - -
78A TYR* 4.2 14.0 - - - -
178A PO4 5.4 6.6 + - - -
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Residues in contact with ASP 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A THR* 6.0 0.2 - - - +
21A LYS* 5.2 8.3 + - - -
31A TYR* 5.4 0.9 - - - -
33A ASN* 2.9 44.5 + - + +
35A GLY* 1.3 72.3 - - - +
37A LEU* 1.3 57.9 + - - +
39A ARG* 3.2 17.9 + - - +
40A GLU* 2.8 38.0 + - + +
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Residues in contact with LEU 37 (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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32A ILE* 4.4 9.2 - - + -
33A ASN 2.9 17.9 + - - +
34A VAL* 3.6 7.6 - - - +
36A ASP* 1.3 73.3 - - - +
38A ALA* 1.3 60.1 + - - +
40A GLU* 4.5 4.9 - - + -
41A GLU* 2.9 50.8 + - + +
43A LEU* 4.4 10.5 - - + -
61A VAL* 4.9 7.4 - - + -
64A GLU* 4.1 17.5 - - + +
65A LEU* 3.6 44.2 - - + -
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Residues in contact with ALA 38 (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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34A VAL 2.9 14.8 + - - +
35A GLY* 3.6 7.0 - - - +
37A LEU* 1.3 77.0 - - - +
39A ARG* 1.3 53.8 + - - +
42A GLN* 2.8 12.8 + - - -
43A LEU* 2.8 40.6 + - + +
44A TYR* 3.7 17.0 - - + -
56A LEU* 3.4 32.8 - - + -
61A VAL* 4.7 1.6 - - + -
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Residues in contact with ARG 39 (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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35A GLY* 3.1 25.2 + - - +
36A ASP* 3.3 21.4 + - - +
38A ALA* 1.3 74.4 - - - +
40A GLU* 1.3 71.6 + - + +
42A GLN* 3.4 16.1 + - - +
44A TYR* 3.2 23.0 + - + +
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Residues in contact with GLU 40 (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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36A ASP* 2.8 26.5 + - + +
37A LEU* 3.9 6.3 - - + +
39A ARG* 1.3 80.1 - - + +
41A GLU* 1.3 74.4 - - + +
42A GLN* 3.8 8.8 + - - +
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Residues in contact with GLU 41 (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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37A LEU* 2.9 33.4 + - + +
40A GLU* 1.3 89.2 - - + +
42A GLN* 1.3 76.8 + - - +
43A LEU* 3.3 26.1 + - + +
60A ARG* 4.5 4.9 + - - -
64A GLU* 3.7 23.6 - - - +
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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