Contacts of the helix formed by residues 37 - 51 (chain B) in PDB entry 1O94
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 LYS 37 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A GLU* 5.5 9.1 + - - +
32B GLY 3.9 11.4 + - - +
33B ALA* 2.9 30.7 + - + +
34B GLY 4.9 0.4 - - - -
36B ASP* 1.3 95.0 - - + +
38B PRO* 1.3 65.7 - - - +
39B GLY 3.3 3.1 - - - -
40B PHE* 3.3 9.1 + - + -
41B GLN* 2.9 22.9 + - - +
73B LEU* 5.0 4.2 - - + +
359B GLY 5.2 5.5 + - - -
361B PRO* 5.0 16.2 - - - +
709B GLU* 3.5 42.0 - - + +
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Residues in contact with PRO 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711A ILE* 3.5 13.7 - - + -
713A TRP* 3.7 37.9 - - + -
34B GLY 5.4 1.1 - - - +
35B SER* 4.4 1.8 - - - +
36B ASP 3.4 9.4 - - - +
37B LYS* 1.3 88.8 - - - +
39B GLY* 1.3 56.9 + - - +
41B GLN* 3.9 7.1 - - + +
42B SER* 2.9 31.9 + - - -
85B ASN* 3.7 42.3 - - + +
88B ALA* 4.6 1.6 - - + +
89B MET 5.3 0.2 + - - -
709B GLU* 3.3 9.4 - - - +
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Residues in contact with GLY 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A TRP* 3.6 10.5 - - - -
38B PRO* 1.3 69.9 - - - +
40B PHE* 1.3 57.8 + - - -
42B SER* 3.3 2.9 + - - -
43B ALA* 2.9 33.8 + - - +
374B TYR* 3.5 31.9 - - - +
709B GLU* 2.7 21.6 + - - -
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Residues in contact with PHE 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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31B ILE* 3.2 46.9 - - + -
32B GLY 4.1 8.3 - - - -
33B ALA* 3.6 13.0 - - + -
37B LYS* 3.3 13.2 + - + +
39B GLY* 1.3 72.0 - - - +
41B GLN* 1.3 62.9 + - - +
44B HIS* 2.9 38.5 + + + +
361B PRO* 3.9 21.3 - - + -
362B MET* 4.4 8.1 - - + -
371B GLY* 3.6 39.9 - - - +
373B GLU* 4.1 4.0 - - - -
374B TYR* 3.8 14.0 - - + +
709B GLU* 2.8 18.8 + - - +
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Residues in contact with GLN 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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31B ILE* 4.1 4.2 - - - +
33B ALA* 3.9 7.9 - - + +
34B GLY 2.9 33.9 + - - +
37B LYS 2.9 17.0 + - - +
38B PRO* 3.9 6.7 - - + +
40B PHE* 1.3 76.8 - - - +
42B SER* 1.3 65.2 + - - +
44B HIS* 4.3 0.2 - - - +
45B ARG* 2.8 65.4 + - - +
58B THR* 3.9 12.9 - - - -
59B GLU* 2.7 25.2 + - - +
75B ALA* 5.2 0.2 - - - +
85B ASN 5.8 1.1 - - - +
86B LEU* 4.7 8.9 - - + +
89B MET* 3.9 21.2 - - + +
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Residues in contact with SER 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713A TRP* 4.4 8.3 - - - -
725A ILE* 3.9 11.2 - - - +
38B PRO 2.9 22.2 + - - -
39B GLY* 3.3 8.0 + - - -
41B GLN* 1.3 79.8 - - - +
43B ALA* 1.3 58.3 + - - +
45B ARG* 4.1 0.5 - - - +
46B SER* 2.8 33.7 + - - -
88B ALA* 3.6 12.1 - - - -
89B MET* 3.6 29.7 - - - +
92B GLU* 4.3 7.3 - - - +
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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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725A ILE* 3.7 13.4 - - + +
727A TYR* 3.6 17.5 - - - +
39B GLY 2.9 21.9 + - - +
40B PHE* 4.2 0.9 - - - +
42B SER* 1.3 71.1 + - - +
44B HIS* 1.3 61.3 + - - +
46B SER* 3.4 5.8 + - - -
47B VAL* 2.8 36.1 + - - +
373B GLU* 3.8 2.9 - - + -
374B TYR* 3.7 29.2 - - + +
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Residues in contact with HIS 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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29B HIS* 3.8 4.8 - - - -
31B ILE* 3.6 25.8 - - + -
40B PHE* 2.9 38.4 + + + +
41B GLN 4.3 0.2 - - - +
43B ALA* 1.3 73.8 - - - +
45B ARG* 1.3 66.4 + - - +
47B VAL* 3.3 14.9 - - - +
48B LYS* 2.9 49.7 + - - +
325B ILE* 4.3 9.2 - - + +
328B PRO* 5.2 4.3 - - + -
362B MET* 3.7 26.7 - - + +
367B ASN* 5.6 0.2 - - - -
370B ALA* 4.6 7.0 - - + -
371B GLY 4.7 0.2 + - - -
373B GLU* 2.7 33.3 + - - +
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Residues in contact with ARG 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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26B GLN* 3.0 36.0 + - - +
29B HIS* 3.0 46.1 + - - -
31B ILE* 3.7 19.1 - - - +
41B GLN* 2.8 42.2 + - - +
44B HIS* 1.3 79.0 - - - +
46B SER* 1.3 65.4 + - - +
48B LYS* 3.3 4.2 + - - +
49B ALA* 3.1 16.8 + - - +
56B LEU* 3.4 20.6 - - + +
57B ASN 3.2 12.7 + - - +
59B GLU* 3.1 21.6 + - - +
89B MET* 3.8 14.4 - - + -
93B VAL* 3.8 19.3 - - + -
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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
----------------------------------------------------------
725A ILE* 4.1 2.8 - - - +
727A TYR* 4.6 2.6 + - - -
42B SER 2.8 23.1 + - - -
43B ALA* 3.4 7.6 + - - -
45B ARG* 1.3 75.8 - - - +
47B VAL* 1.3 67.7 + - - +
49B ALA* 3.6 7.7 - - - +
50B GLU* 3.0 23.4 + - - +
92B GLU* 3.4 42.5 - - - +
93B VAL* 4.1 3.3 - - - +
96B TYR* 3.8 11.9 - - - -
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
727A TYR* 3.1 37.7 - - + +
43B ALA 2.8 13.9 + - - +
44B HIS* 3.3 18.6 - - - +
46B SER* 1.3 78.8 + - - +
48B LYS* 1.3 59.2 + - - +
50B GLU* 3.4 7.4 + - - +
51B GLY 2.8 22.7 + - - -
328B PRO* 4.0 23.1 - - + -
329B PHE* 3.4 15.2 - - + -
373B GLU* 4.2 17.7 - - + +
379B HIS* 4.1 14.4 - - + -
380B PRO* 4.4 11.4 - - + -
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Residues in contact with LYS 48 (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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26B GLN* 2.8 34.3 - - - +
29B HIS* 2.9 20.4 + - - -
44B HIS* 2.9 43.0 + - - +
45B ARG* 3.3 4.2 + - - +
46B SER 3.2 0.2 - - - -
47B VAL* 1.3 75.7 - - - +
49B ALA* 1.3 66.1 + - - +
51B GLY 3.0 8.0 + - - -
52B GLY 3.1 10.2 + - - -
53B TRP* 3.2 20.1 + - + -
56B LEU* 3.5 17.7 - - + -
324B SER* 3.0 34.8 + - - +
325B ILE* 4.3 0.2 - - - +
328B PRO* 3.7 26.7 - - + -
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Residues in contact with ALA 49 (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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21B ARG* 2.8 27.4 + - - +
45B ARG 3.1 10.9 + - - +
46B SER* 3.2 12.3 + - - +
48B LYS* 1.3 74.5 - - - +
50B GLU* 1.3 64.1 + - - +
52B GLY* 3.0 3.5 + - - -
53B TRP 4.1 0.2 - - - -
56B LEU* 3.8 15.1 - - + +
93B VAL* 3.8 11.0 - - - +
96B TYR* 3.6 20.6 - - + +
98B ALA* 3.8 19.3 - - + -
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Residues in contact with GLU 50 (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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727A TYR* 5.7 0.7 - - - -
46B SER 3.0 11.5 + - - +
47B VAL* 3.6 9.5 - - - +
49B ALA* 1.3 75.5 - - - +
51B GLY* 1.3 57.9 + - - +
52B GLY* 3.1 5.7 + - - -
96B TYR* 3.6 39.1 + - + +
329B PHE* 3.7 12.1 - - + -
332B GLN* 4.0 12.9 + - - +
379B HIS* 2.7 31.8 + - - -
382B LYS* 2.7 30.7 + - - -
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Residues in contact with GLY 51 (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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47B VAL 2.8 15.3 + - - -
48B LYS 3.0 9.1 + - - -
50B GLU* 1.3 74.8 - - - +
52B GLY* 1.3 54.6 + - - -
53B TRP 3.6 0.7 - - - -
328B PRO 3.7 12.3 - - - -
329B PHE* 3.6 22.1 - - - -
331B PRO* 3.5 10.9 - - - +
332B GLN* 3.1 28.9 + - - +
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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