Contacts of the helix formed by residues 41 - 56 (chain B) in PDB entry 4OA5
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 41 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B HIS* 4.4 6.5 - - - -
39B GLN 3.6 1.6 + - - -
40B LEU* 1.3 76.4 - - - +
42B THR* 1.3 61.3 + - - -
43B VAL 3.2 2.9 - - - -
44B GLU* 3.1 19.5 + - - -
45B GLY 2.9 23.0 + - - -
69B PHE* 3.6 7.6 - - - -
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Residues in contact with THR 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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14B ASN* 2.9 26.1 + - - -
18B ALA* 3.5 8.1 - - - +
19B VAL* 3.0 48.2 + - + +
25B LEU* 3.6 24.0 - - + -
28B HIS* 5.3 4.2 + - + -
41B GLY* 1.3 71.9 - - - -
43B VAL* 1.3 60.3 + - - +
46B GLN 3.2 12.1 + - - -
69B PHE* 4.1 18.8 - - + -
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B LEU* 3.5 52.0 - - + +
14B ASN* 3.7 25.1 + - - +
17B PHE* 3.8 14.3 - - + +
18B ALA* 3.9 3.4 - - + +
41B GLY 3.2 0.8 - - - -
42B THR* 1.3 75.5 + - - +
44B GLU* 1.3 74.6 + - - +
46B GLN* 3.2 5.2 + - - +
47B MET* 3.1 20.4 + - - +
313B IOD 4.4 16.8 - - + -
203C THR* 4.8 7.4 + - - +
204C ILE 6.0 1.3 - - - +
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Residues in contact with GLU 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 4.1 24.9 - - + -
41B GLY* 3.1 30.7 + - - +
43B VAL* 1.3 88.1 + - - +
45B GLY* 1.3 62.5 + - - +
47B MET* 3.2 10.4 + - - +
48B LEU* 3.1 25.3 + - - +
162B ASP* 5.7 1.6 - - - +
207B THR* 4.4 24.6 - - + +
209B GLU* 4.5 13.9 - - - +
211B MET* 4.5 10.8 - - + +
313B IOD 4.4 4.0 - - + -
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Residues in contact with GLY 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 3.7 6.3 - - - -
40B LEU* 4.2 11.6 - - - +
41B GLY 2.9 16.0 + - - -
42B THR 3.4 2.9 + - - -
43B VAL 3.2 0.2 - - - -
44B GLU* 1.3 78.2 - - - +
46B GLN* 1.3 59.6 + - - +
48B LEU* 3.4 6.1 + - - +
49B GLN* 3.2 24.9 + - - +
69B PHE* 4.9 0.4 - - - -
73B CYS* 4.0 24.3 - - - +
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Residues in contact with GLN 46 (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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16B LEU 4.8 0.2 + - - -
17B PHE* 3.4 35.2 - - - +
18B ALA 3.2 9.0 - - - -
19B VAL* 3.5 8.0 + - + +
42B THR 3.2 12.0 + - - +
43B VAL 3.7 2.5 - - - +
44B GLU 3.2 0.4 - - - -
45B GLY* 1.3 73.0 - - - +
47B MET* 1.3 64.9 + - - +
49B GLN* 3.2 14.8 + - - +
50B LEU* 3.0 21.7 + - + +
197C LYS* 3.0 32.4 + - - +
201C LEU* 3.8 20.3 - - + +
202C SER* 2.8 34.9 + - - +
203C THR* 5.5 1.3 - - - -
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Residues in contact with MET 47 (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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43B VAL 3.1 7.1 + - - +
44B GLU* 3.2 9.8 + - - +
46B GLN* 1.3 77.0 - - - +
48B LEU* 1.3 63.3 + - + +
50B LEU* 3.2 10.1 + - + +
51B LEU* 3.0 29.5 + - + +
211B MET* 6.5 1.1 - - + -
313B IOD 3.7 30.5 - - + -
203C THR* 4.3 16.9 + - + +
205C ILE* 5.9 1.8 - - + -
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.4 26.5 - - + -
44B GLU 3.1 16.6 + - - +
45B GLY* 3.6 7.9 - - - +
46B GLN 3.2 0.4 - - - -
47B MET* 1.3 76.2 - - + +
49B GLN* 1.3 58.7 + - - +
51B LEU* 3.2 14.3 + - + +
52B ILE* 2.9 35.4 + - + +
70B SER* 4.8 3.4 - - - +
73B CYS* 5.9 0.7 - - + -
74B MET* 3.8 35.2 - - + -
132B MET* 4.8 5.8 - - + +
134B PHE* 4.1 17.9 - - + -
160B VAL* 3.9 28.3 - - + -
211B MET* 4.5 10.1 - - + -
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Residues in contact with GLN 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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19B VAL* 3.7 25.3 - - - +
21B THR* 6.2 1.4 - - - +
45B GLY 3.2 8.3 + - - +
46B GLN* 3.2 24.9 + - - +
48B LEU* 1.3 78.7 - - - +
50B LEU* 1.3 56.1 + - - +
52B ILE* 3.2 4.2 + - - +
53B ARG* 2.9 30.7 + - - +
73B CYS* 2.9 34.7 + - - +
76B HIS* 3.9 18.2 - - - +
77B ALA* 3.7 19.4 - - + +
305B IOD 3.7 21.5 - - + +
201C LEU* 3.8 9.0 - - + +
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Residues in contact with LEU 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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46B GLN 3.0 12.5 + - - +
47B MET* 3.2 10.1 + - - +
49B GLN* 1.3 76.1 - - - +
51B LEU* 1.3 60.2 + - + +
53B ARG* 3.3 1.0 + - - +
54B MET* 2.8 59.4 + - + +
51C LEU* 6.1 0.2 - - + -
201C LEU* 3.5 29.5 - - + +
202C SER 5.7 0.9 - - - -
203C THR* 3.4 34.8 - - + +
205C ILE* 5.7 0.7 - - + -
213C VAL* 3.9 17.5 - - + +
215C ILE* 3.4 28.7 - - + +
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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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47B MET* 3.0 21.7 + - + +
48B LEU* 3.2 24.4 + - + +
50B LEU* 1.3 78.3 - - + +
52B ILE* 1.3 63.7 + - + +
54B MET* 3.3 10.6 + - + +
55B ALA* 3.0 28.2 + - - +
132B MET* 5.6 2.0 - - + -
158B LEU* 4.5 7.6 - - + -
160B VAL* 4.4 9.6 - - + -
205B ILE* 6.2 2.2 - - + -
211B MET* 5.7 1.3 - - + -
213B VAL* 3.7 35.0 - - + -
50C LEU* 6.2 0.4 - - + -
51C LEU* 5.5 5.2 - - + -
54C MET* 3.6 32.6 - - + +
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Residues in contact with ILE 52 (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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48B LEU 2.9 22.0 + - - +
49B GLN* 3.6 4.9 - - - +
51B LEU* 1.3 76.3 - - - +
53B ARG* 1.3 63.4 + - - +
56B GLY* 3.1 3.6 + - - -
57B ILE* 3.1 39.1 + - + +
60B ILE* 3.6 12.3 - - + -
74B MET* 3.5 47.6 - - + +
77B ALA* 3.8 21.1 - - + +
78B LEU* 3.8 24.0 - - + -
79B PRO* 5.5 0.2 - - + -
132B MET* 3.9 21.8 - - + -
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Residues in contact with ARG 53 (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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49B GLN 2.9 14.6 + - - +
52B ILE* 1.3 76.0 - - - +
54B MET* 1.3 66.7 + - - +
56B GLY* 3.3 10.3 + - - -
76B HIS 4.0 3.6 + - - -
77B ALA* 3.3 27.3 + - - +
304B IOD 3.6 29.6 - - + +
305B IOD 3.1 35.3 - - - +
201C LEU* 4.2 11.3 - - + +
215C ILE* 3.6 17.5 - - + -
217C LEU* 4.1 19.7 - - + +
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Residues in contact with MET 54 (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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50B LEU* 2.8 62.2 + - + +
51B LEU* 3.3 9.2 + - + +
53B ARG* 1.3 74.2 - - - +
55B ALA* 1.3 61.8 + - - +
56B GLY 3.2 1.1 + - - -
51C LEU* 3.9 30.7 - - + +
54C MET* 3.4 26.2 - - + +
55C ALA* 3.5 25.5 - - + +
158C LEU* 4.1 20.2 - - + -
213C VAL* 3.8 16.6 - - + -
215C ILE* 3.7 11.8 - - + +
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Residues in contact with ALA 55 (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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51B LEU 3.0 14.2 + - - +
54B MET* 1.3 78.0 - - - +
56B GLY* 1.3 64.2 + - - +
57B ILE* 3.3 23.0 + - + +
154B ARG* 4.4 9.4 + - - -
156B GLY 5.9 2.5 - - - +
158B LEU* 3.9 15.9 - - + -
54C MET* 3.5 24.9 - - + +
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Residues in contact with GLY 56 (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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52B ILE 3.1 7.3 + - - -
53B ARG 3.3 6.7 + - - -
54B MET 3.2 5.3 + - - -
55B ALA* 1.3 77.5 - - - +
57B ILE* 1.3 65.9 + - - +
58B HIS* 3.1 21.9 + - - -
79B PRO* 6.0 0.2 - - - -
131B ASP* 4.8 0.9 - - - +
154B ARG* 5.2 3.7 + - - -
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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