Contacts of the helix formed by residues 41 - 52 (chain B) in PDB entry 5OIV
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 SER 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B MET 4.1 0.4 + - - -
40B TRP* 1.3 71.5 - - - +
42B TRP* 1.3 64.5 + - - +
44B ALA* 3.2 12.1 + - - +
45B ALA 3.3 5.9 + - - -
66B LEU* 3.9 12.0 - - - +
76B ILE* 3.5 13.1 + - - +
77B PRO 3.4 23.6 - - - -
78B HIS* 2.8 18.4 + - - -
80B VAL 5.7 0.2 - - - +
115B GLN* 3.7 12.3 + - - +
119B HIS* 3.0 35.5 + - - -
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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
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41B SER* 1.3 80.9 - - - +
43B ALA* 1.3 69.4 + - - +
45B ALA* 3.3 4.9 + - - +
46B PHE* 3.0 48.4 + + - -
115B GLN* 3.1 35.3 + - - +
116B PRO* 3.8 36.6 - - + +
118B VAL* 3.6 22.4 - - + -
119B HIS* 4.4 1.3 - - - -
179B SER 4.6 4.7 - - - -
180B GLY* 3.7 30.9 - - - -
181B MET* 5.3 5.4 - - + -
254B PHE* 5.2 2.9 - + - -
258B ILE* 4.5 13.0 - - + -
376B TRP* 4.7 13.2 - + - -
383B VAL* 5.3 4.0 - - + -
384B LEU* 5.1 9.4 - - + -
387B LEU* 4.9 6.5 - - + -
436B TRP* 3.4 24.8 - + - -
502B GOL 2.9 22.7 + - - -
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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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31B ALA* 4.2 19.5 - - + -
40B TRP* 3.4 24.8 + - + +
41B SER 3.2 0.4 - - - -
42B TRP* 1.3 83.7 - - - +
44B ALA* 1.3 50.4 + - - +
46B PHE* 3.1 4.0 + - - +
47B VAL* 2.7 43.3 + - + +
436B TRP* 3.7 29.5 - - + +
502B GOL 4.6 1.8 - - - -
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Residues in contact with ALA 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 THR 6.1 0.2 - - - -
39B MET* 4.0 30.5 - - + -
40B TRP 2.7 22.0 + - - +
41B SER 3.2 6.0 + - - +
43B ALA* 1.3 74.3 - - - +
45B ALA* 1.3 55.6 + - - +
47B VAL* 3.3 9.0 + - - +
48B ALA* 2.9 30.1 + - - +
62B GLU* 3.9 11.5 - - + +
63B LEU* 4.2 3.2 - - + +
66B LEU* 4.3 14.1 - - + -
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Residues in contact with ALA 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B SER 3.3 2.8 + - - -
42B TRP 3.3 2.6 + - - +
43B ALA 3.2 0.6 - - - -
44B ALA* 1.3 78.6 - - - +
46B PHE* 1.3 62.2 + - + +
48B ALA 3.2 1.6 + - - -
49B ILE* 3.1 20.8 + - + +
63B LEU* 4.3 6.9 - - - +
118B VAL* 3.5 41.5 - - + +
119B HIS* 3.9 22.4 - - + -
122B ALA* 3.3 20.1 - - + +
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Residues in contact with PHE 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B TRP* 3.0 49.5 + + - -
43B ALA 3.1 6.5 + - - +
45B ALA* 1.3 75.0 - - - +
47B VAL* 1.3 62.2 + - - +
49B ILE* 3.1 17.6 + - + +
50B GLY 3.0 18.4 + - - -
118B VAL* 4.0 25.8 - - + -
121B ILE* 6.3 0.4 - - + -
383B VAL* 3.5 28.9 - - + -
386B TRP* 3.8 36.3 - + + -
387B LEU* 4.7 11.9 - - + -
436B TRP* 3.6 32.5 - + + +
439B ALA* 3.2 12.3 - - + +
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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
----------------------------------------------------------
20B LEU* 4.4 8.5 - - + +
29B THR* 3.7 36.6 - - + +
30B THR 5.2 0.9 - - - +
31B ALA* 5.8 0.7 - - - -
43B ALA* 2.7 29.1 + - + +
44B ALA* 3.6 9.2 - - - +
46B PHE* 1.3 74.0 - - - +
48B ALA* 1.3 57.1 + - - +
50B GLY* 3.1 2.6 + - - -
51B LEU* 2.8 41.8 + - + +
62B GLU* 3.9 7.4 - - - +
435B SER* 3.8 32.1 - - - -
436B TRP 4.8 1.3 - - - +
439B ALA* 4.3 5.6 - - - -
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Residues in contact with ALA 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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44B ALA 2.9 17.3 + - - +
45B ALA 3.2 5.3 + - - +
47B VAL* 1.3 77.6 - - - +
49B ILE* 1.3 57.8 + - - +
51B LEU* 3.3 9.4 + - - -
52B ALA* 3.0 26.7 + - - +
59B ALA* 3.5 28.9 - - - +
62B GLU* 4.4 2.9 - - + -
63B LEU* 3.9 19.7 - - + -
122B ALA* 4.3 2.5 - - + -
126B ILE* 4.2 11.5 - - + +
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Residues in contact with ILE 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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45B ALA* 3.1 15.7 + - + +
46B PHE* 3.1 21.2 + - + +
48B ALA* 1.3 76.4 - - - +
50B GLY* 1.3 60.7 + - - +
52B ALA* 3.4 6.7 + - - +
53B PRO* 3.2 18.9 - - - +
118B VAL* 5.4 2.0 - - + +
121B ILE* 4.3 4.7 - - + -
122B ALA* 3.5 31.6 - - + +
125B ARG* 4.1 14.4 - - + -
129B HIS* 4.9 0.9 + - - -
386B TRP* 3.7 35.9 - - + -
439B ALA* 4.9 2.7 - - + +
443B ASP* 3.6 37.7 - - + +
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Residues in contact with GLY 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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20B LEU* 3.8 8.1 - - - -
46B PHE 3.0 11.1 + - - -
47B VAL 3.1 3.3 + - - -
49B ILE* 1.3 78.0 - - - +
51B LEU* 1.3 59.1 + - - +
53B PRO* 3.4 14.7 - - - +
54B LEU* 3.7 4.7 - - - +
439B ALA* 3.6 31.8 - - - +
442B LEU* 3.6 18.7 - - - +
443B ASP 5.1 0.2 - - - -
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Residues in contact with LEU 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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20B LEU* 4.2 24.7 - - + +
21B ARG* 5.7 2.2 - - - +
24B ASP* 6.2 0.2 - - - +
29B THR* 4.5 4.3 - - + +
47B VAL* 2.8 37.0 + - + +
48B ALA 3.8 4.0 - - - +
49B ILE 3.3 0.2 - - - -
50B GLY* 1.3 76.3 - - - +
52B ALA* 1.3 60.4 + - - +
53B PRO 3.3 0.2 - - - -
54B LEU* 2.8 33.3 + - + +
55B SER* 2.8 17.0 + - - +
58B ARG* 3.8 47.3 - - + +
59B ALA* 3.8 14.4 - - + +
62B GLU* 4.1 5.8 - - + +
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Residues in contact with ALA 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B ALA 3.0 16.3 + - - +
49B ILE* 3.7 6.3 - - - +
51B LEU* 1.3 75.6 - - - +
53B PRO* 1.3 64.1 - - + +
54B LEU 3.3 0.9 + - - -
55B SER 3.8 6.3 + - - -
56B VAL* 3.9 15.4 + - + +
59B ALA* 4.0 7.9 - - - -
125B ARG 4.4 0.7 - - - +
126B ILE* 4.1 23.8 - - + +
129B HIS* 3.4 32.9 + - + +
133B ARG* 6.1 0.3 - - - +
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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