Contacts of the helix formed by residues 31 - 47 (chain B) in PDB entry 4OIN
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 GLY 31 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ARG* 2.7 34.1 + - - -
30B ARG* 1.3 76.9 - - - +
32B PHE* 1.3 60.9 + - - +
33B GLY 3.1 7.0 + - - -
34B VAL* 3.3 6.5 + - - +
35B THR* 3.2 11.9 + - - -
193B ASP* 3.0 15.2 + - - -
2001B MG 4.5 0.8 - - - -
854C PRO* 5.7 0.4 - - - -
856C GLU* 4.5 3.8 - - - -
857C ASP* 4.7 5.8 - - - -
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Residues in contact with PHE 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A ILE* 3.7 29.4 - - + -
46A SER* 4.8 5.2 - - - -
47A SER* 3.2 28.3 - - - -
217A ILE* 4.0 10.8 - - + -
221A HIS* 3.3 43.5 - + + +
28B LEU* 4.0 17.6 - - + +
29B GLU* 3.1 40.9 + - + +
30B ARG 3.3 8.7 - - - -
31B GLY* 1.3 74.1 - - - +
33B GLY* 1.3 64.5 + - - +
34B VAL 3.3 0.2 - - - -
35B THR* 3.6 18.2 - - + -
36B LEU* 3.1 29.3 + - + +
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Residues in contact with GLY 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B LEU* 4.1 11.2 - - - +
32B PHE* 1.3 76.8 - - - +
34B VAL* 1.3 57.2 + - - +
37B GLY* 3.1 19.6 + - - -
179B PHE* 4.2 0.2 - - - -
181B VAL* 3.5 21.3 - - - +
193B ASP* 3.0 23.5 + - - +
195B LEU* 3.3 19.0 - - - +
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Residues in contact with VAL 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ARG* 3.3 36.1 - - - +
31B GLY* 3.3 3.1 + - - +
33B GLY* 1.3 73.6 - - - +
35B THR* 1.3 67.0 + - - +
36B LEU 3.3 0.4 - - - -
37B GLY 3.8 0.7 - - - -
38B ASN* 3.4 35.4 + - - +
39B PRO* 4.1 0.5 - - - +
179B PHE* 4.1 12.3 - - + -
181B VAL* 3.6 22.2 - - + -
193B ASP* 5.5 0.7 - - - +
857C ASP* 5.3 2.5 - - - +
978C ARG* 3.8 29.2 - - + +
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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
----------------------------------------------------------
39A PRO* 4.0 24.2 - - + +
42A ARG* 2.7 34.9 + - - +
43A ILE* 4.1 19.4 - - + +
218A LEU* 4.5 7.5 - - + +
31B GLY 3.2 7.0 + - - -
32B PHE* 3.3 33.5 + - + -
34B VAL* 1.3 80.9 - - - +
36B LEU* 1.3 58.5 + - + +
39B PRO* 3.1 24.9 - - - +
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Residues in contact with LEU 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A LEU* 3.7 27.1 - - + -
221A HIS* 3.9 25.8 - - + +
222A LEU* 4.6 16.8 - - + -
225A PHE* 3.9 13.5 - - + -
25B LEU* 3.7 29.6 - - + -
28B LEU* 4.2 15.5 - - + -
32B PHE* 3.1 19.9 + - + +
35B THR* 1.3 80.1 - - + +
37B GLY* 1.3 63.5 + - - +
38B ASN 3.5 0.2 - - - -
39B PRO* 3.2 9.1 - - - +
40B LEU* 3.2 24.5 - - + +
195B LEU* 4.1 11.0 - - + -
218B LEU* 5.6 2.8 - - + +
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Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B GLY 3.1 17.1 + - - -
34B VAL 3.7 0.2 + - - -
35B THR 3.6 0.2 - - - -
36B LEU* 1.3 79.2 - - - +
38B ASN* 1.3 57.4 + - - +
40B LEU* 3.6 5.4 + - - +
41B ARG* 3.0 28.9 + - - +
179B PHE* 3.8 24.5 - - - +
195B LEU* 4.2 9.4 - - - +
197B LEU* 5.1 4.4 - - - +
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Residues in contact with ASN 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B VAL* 3.4 15.2 + - - +
37B GLY* 1.3 72.1 - - - +
39B PRO* 1.3 73.0 - - + +
41B ARG* 3.2 10.3 + - - +
42B ARG* 2.9 34.2 + - + +
179B PHE* 3.2 29.9 - - - -
978C ARG* 2.9 28.6 + - - +
979C THR* 3.5 31.8 - - - +
981C GLU* 4.9 4.2 - - - +
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Residues in contact with PRO 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A THR* 3.8 26.7 - - + +
39A PRO* 3.3 24.5 - - + -
218A LEU* 6.0 0.2 - - + -
34B VAL 4.1 0.2 - - - +
35B THR 3.1 27.4 - - - +
36B LEU* 3.2 7.0 - - - +
38B ASN* 1.3 93.0 - - + +
40B LEU* 1.3 56.0 + - - +
42B ARG* 3.1 8.0 + - - +
43B ILE* 2.8 35.3 + - - +
218B LEU* 4.3 19.3 - - + -
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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
----------------------------------------------------------
222A LEU* 4.6 2.0 - - + -
225A PHE* 3.7 32.5 - - + -
36B LEU* 3.2 22.6 + - + +
37B GLY 3.8 3.8 - - - +
38B ASN 3.3 0.2 - - - -
39B PRO* 1.3 78.3 - - - +
41B ARG* 1.3 53.6 + - - +
43B ILE* 3.3 4.5 + - + +
44B LEU* 2.7 49.5 + - + +
195B LEU* 5.5 0.2 - - + -
197B LEU* 4.0 11.2 - - + -
211B LEU* 3.9 17.5 - - + -
214B ALA* 4.4 7.9 - - + +
215B VAL* 3.7 30.7 - - + +
218B LEU* 4.2 21.8 - - + -
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Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B GLY 3.0 18.9 + - - +
38B ASN* 3.2 10.7 + - - +
40B LEU* 1.3 76.4 - - - +
42B ARG* 1.3 71.6 + - - +
44B LEU* 3.9 1.3 - - - +
45B LEU* 3.1 46.6 + - + +
177B VAL* 3.6 48.0 + - + -
178B ALA* 5.6 0.2 - - - +
179B PHE* 4.2 22.2 - - + -
197B LEU* 5.5 0.2 - - - +
981C GLU* 4.8 11.5 + - - -
854D ALA* 4.5 12.7 - - - +
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Residues in contact with ARG 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A GLY* 3.0 30.3 + - - -
34A VAL* 3.6 23.9 - - - +
35A THR* 2.8 38.1 + - - +
38B ASN* 2.9 26.6 + - + +
39B PRO* 3.1 6.0 + - - +
41B ARG* 1.3 88.0 - - - +
43B ILE* 1.3 52.2 + - - +
45B LEU* 3.9 3.8 - - - +
46B SER* 2.6 39.7 + - - +
979C THR 5.6 1.3 - - - -
981C GLU* 3.1 42.2 + - - +
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Residues in contact with ILE 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A PHE* 4.1 12.6 - - + -
35A THR* 3.8 21.5 - - + -
39B PRO 2.8 25.3 + - - +
40B LEU* 3.8 6.1 - - - +
42B ARG* 1.3 73.2 - - - +
44B LEU* 1.3 60.1 + - - +
46B SER* 3.9 4.5 - - - -
47B SER* 2.8 30.7 + - - +
48B ILE* 3.7 3.4 + - + +
214B ALA* 3.7 32.3 - - + +
217B ILE* 3.9 26.5 - - + -
218B LEU* 3.7 39.0 - - + +
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Residues in contact with LEU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 2.7 35.3 + - + +
41B ARG 3.9 0.4 - - - +
42B ARG 3.4 0.2 - - - -
43B ILE* 1.3 73.0 - - - +
45B LEU* 1.3 62.3 + - - +
48B ILE* 3.3 21.3 - - + +
172B SER* 3.9 1.6 + - - -
174B VAL* 3.4 19.8 - - + +
177B VAL* 3.7 28.9 - - + -
197B LEU* 4.6 3.4 - - + -
199B ILE* 3.7 24.9 - - + -
210B ALA* 3.4 47.3 - - + +
211B LEU* 3.7 14.6 - - + +
214B ALA* 3.7 9.6 - - + -
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Residues in contact with LEU 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ARG* 3.1 52.4 + - + +
42B ARG* 4.0 3.6 - - - +
44B LEU* 1.3 78.7 - - - +
46B SER* 1.3 61.5 + - - +
48B ILE 5.1 0.4 + - - -
149B GLY* 3.9 0.9 - - - -
172B SER* 3.3 22.0 + - - -
174B VAL* 4.1 14.6 - - + +
175B ARG 4.9 0.9 - - - +
176B ARG* 4.5 4.9 - - - -
177B VAL* 3.8 30.7 - - + +
851D LEU* 4.2 20.4 - - + +
854D ALA* 4.2 18.2 - - + -
855D HIS* 3.6 14.5 + - + +
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Residues in contact with SER 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ARG* 4.9 13.3 + - - -
32A PHE* 4.4 5.9 - - - -
42B ARG 2.6 24.7 + - - -
43B ILE* 3.9 0.5 - - - -
45B LEU* 1.3 79.6 - - - +
47B SER* 1.3 69.2 + - - +
48B ILE 3.6 1.1 - - - -
148B VAL* 3.5 7.8 - - - +
149B GLY* 3.1 25.0 + - - -
855D HIS* 3.7 21.0 - - - -
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Residues in contact with SER 47 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLU* 5.6 0.7 - - - +
32A PHE* 3.0 36.8 - - - -
43B ILE* 2.8 19.2 + - - -
46B SER* 1.3 75.8 + - - +
48B ILE* 1.3 63.3 + - - +
49B PRO* 3.3 9.7 - - - +
148B VAL* 3.5 14.7 - - - +
217B ILE* 3.8 25.6 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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