Contacts of the helix formed by residues 32 - 43 (chain B) in PDB entry 2IVF
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 GLN 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128A GLN* 3.6 3.1 - - + +
851A ARG* 5.4 2.2 - - - -
867A LEU* 3.9 27.6 - - + -
30B GLY* 3.3 10.1 + - - +
31B CYS* 1.3 78.4 - - - +
33B THR* 1.3 63.9 + - - +
34B CYS 3.2 2.5 - - - -
35B THR* 2.8 26.8 + - - +
36B VAL* 3.1 14.9 + - - +
56B VAL* 2.8 35.9 + - - +
57B THR* 5.0 0.2 - - - +
128B TYR* 2.7 30.4 + - - -
129B ASN* 3.3 26.7 + - - +
132B GLU* 4.8 2.9 + - - +
146B TYR* 6.3 0.6 - - - -
1358B SF4 3.3 13.7 - - - -
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Residues in contact with THR 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLN* 4.1 2.9 - - - +
127A CYS* 3.2 11.7 - - - +
128A GLN* 3.0 24.0 + - - +
131A SER* 3.4 27.8 - - - +
31B CYS* 3.1 18.3 + - - -
32B GLN* 1.3 76.4 - - - +
34B CYS* 1.3 57.3 + - - +
36B VAL* 3.2 4.6 - - - +
37B ALA* 2.8 29.1 + - - +
229B GLN* 3.3 23.8 - - + +
231B PRO* 3.6 17.6 - - + +
1358B SF4 3.9 0.2 - - - -
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Residues in contact with CYS 34 (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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32B GLN 4.5 0.4 - - - -
33B THR* 1.3 78.9 - - - +
35B THR* 1.3 61.2 + - - +
37B ALA* 3.5 7.8 - - - +
38B CYS* 3.1 19.1 + - - +
54B ASN* 3.1 35.5 - - - +
56B VAL* 3.3 18.6 - - - -
226B CYS* 3.5 20.7 - - + +
229B GLN* 5.6 1.1 - - - -
235B ARG* 3.4 21.3 - - - +
1358B SF4 2.2 37.3 - - - -
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Residues in contact with THR 35 (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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867A LEU* 3.8 20.4 - - + -
32B GLN* 2.8 29.9 + - - -
34B CYS* 1.3 75.8 - - - +
36B VAL* 1.3 59.6 + - + +
38B CYS* 3.5 3.3 + - - +
39B LYS* 3.0 33.3 + - + +
52B ARG* 4.1 12.1 - - + -
54B ASN* 3.2 30.0 + - - +
56B VAL* 3.5 6.4 - - - +
128B TYR* 3.3 23.3 + - + +
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Residues in contact with VAL 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLN* 3.6 30.1 - - + +
131A SER* 3.6 24.9 - - - +
132A ALA* 4.0 7.9 - - + -
863A HIS* 4.5 7.2 - - - +
864A LEU* 4.3 1.8 - - + -
867A LEU* 3.6 35.0 - - + -
32B GLN 3.1 6.4 + - - +
33B THR 3.2 13.5 - - - +
35B THR* 1.3 75.3 - - - +
37B ALA* 1.3 64.8 + - - +
39B LYS* 4.2 4.3 - - - -
40B ASN* 2.8 43.3 + - - +
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Residues in contact with ALA 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ARG* 4.6 1.1 + - - +
131A SER 5.4 1.6 - - - -
33B THR 2.8 21.4 + - - +
34B CYS* 3.5 7.4 - - - +
35B THR 3.3 0.2 - - - -
36B VAL* 1.3 73.6 - - - +
38B CYS* 1.3 64.6 + - - +
40B ASN* 3.7 2.4 + - - +
41B ILE* 3.6 24.8 + - - +
225B ALA* 3.6 22.0 - - - +
229B GLN* 3.3 39.7 - - + +
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Residues in contact with CYS 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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34B CYS 3.1 8.8 + - - +
35B THR 3.7 7.9 - - - +
37B ALA* 1.3 81.8 - - - +
39B LYS* 1.3 58.9 + - - +
41B ILE 3.2 2.4 + - - -
42B TRP* 2.9 39.6 + - - -
43B THR* 5.1 2.7 - - - -
53B TRP* 3.8 23.1 - - - -
54B ASN* 4.0 11.2 - - + +
1359B SF4 2.3 51.5 - - - -
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Residues in contact with LYS 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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863A HIS* 3.7 22.4 - - + +
866A ARG* 6.5 0.9 - - - +
867A LEU* 6.6 0.2 - - + -
35B THR* 3.0 20.7 + - + +
36B VAL* 3.3 7.8 + - - +
38B CYS* 1.3 77.6 - - - +
40B ASN* 1.3 63.1 + - - +
41B ILE 4.0 0.2 - - - -
42B TRP 3.6 0.2 + - - -
43B THR* 2.7 64.2 + - - +
44B LYS* 3.4 12.3 + - + +
48B THR 3.1 4.2 + - - -
49B GLU* 3.0 26.3 + - - +
51B MET 2.6 28.2 + - - +
52B ARG* 4.3 21.8 - - + +
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Residues in contact with ASN 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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104A TRP* 3.8 18.9 + - - +
105A ARG* 3.9 18.4 - - + +
106A GLU 6.0 0.4 - - - +
131A SER 4.3 8.5 - - - +
132A ALA* 3.9 5.7 - - - +
134A ASN* 2.9 17.9 - - - +
135A ASN* 2.8 23.2 + - - -
863A HIS* 3.0 26.6 + - - -
36B VAL* 2.8 35.5 + - - +
37B ALA* 4.4 2.2 - - - +
39B LYS* 1.3 78.6 - - - +
41B ILE* 1.3 59.6 + - - +
44B LYS* 3.2 19.1 + - - +
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Residues in contact with ILE 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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71A GLU* 4.0 21.6 - - + +
72A TRP* 4.1 16.8 - - + -
104A TRP* 4.3 13.9 + - + -
105A ARG* 3.4 34.1 - - - +
37B ALA 3.6 7.6 + - - +
38B CYS 3.2 2.7 + - - +
39B LYS 4.0 0.2 - - - -
40B ASN* 1.3 80.1 - - - +
42B TRP* 1.3 105.6 + - + +
43B THR 3.8 0.4 - - - -
44B LYS* 5.4 1.2 + - - +
45B ARG* 6.0 0.3 - - - +
217B ARG* 3.9 13.9 - - - +
225B ALA* 3.6 31.2 - - + -
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Residues in contact with TRP 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A TYR* 3.4 33.9 - + + -
71A GLU* 4.1 8.5 - - + -
72A TRP* 4.5 5.6 - - + -
38B CYS* 2.9 32.7 + - - +
41B ILE* 1.3 106.9 - - + +
43B THR* 1.3 58.4 + - + +
44B LYS 3.6 2.2 - - - -
45B ARG* 2.8 37.5 + - - +
53B TRP* 3.2 24.7 - + + -
212B ILE* 3.8 25.4 - - + -
214B CYS* 3.4 36.9 - - + -
216B PRO* 3.6 27.4 - - + -
217B ARG* 4.6 8.3 - - - -
1359B SF4 3.6 18.9 - - - -
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Residues in contact with THR 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B CYS* 4.6 2.5 - - - -
39B LYS* 2.7 74.0 + - - +
42B TRP* 1.3 85.8 - - + +
44B LYS* 1.3 59.2 + - - +
48B THR* 3.1 24.5 + - - +
49B GLU* 3.8 4.2 - - - -
51B MET* 3.2 12.7 + - + +
52B ARG* 5.3 0.5 - - - -
53B TRP* 3.5 43.0 + - + +
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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