Contacts of the helix formed by residues 55 - 68 (chain A) 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 55 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A LEU* 2.8 18.5 + - - +
52A ALA 4.2 0.4 - - - -
53A PRO 3.8 0.6 - - - -
54A LEU* 1.3 78.7 - - - +
56A VAL* 1.3 64.1 + - - +
57A GLU* 3.6 8.3 + - - +
58A ARG* 3.1 30.9 + - - +
59A ALA* 2.9 17.5 + - - +
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Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ALA* 3.9 17.0 + - - +
55A SER* 1.3 72.1 - - - +
57A GLU* 1.3 64.7 + - - +
59A ALA* 3.2 7.5 + - - +
60A VAL* 3.0 24.3 + - + +
126A ILE* 4.2 20.6 - - + +
129A HIS* 4.4 6.3 - - + +
130A ALA* 4.1 20.6 - - + +
133A ARG* 5.0 4.0 - - + -
137A THR* 3.6 38.4 - - + +
140A VAL* 4.0 17.0 - - + -
141A ALA* 4.5 2.0 - - + -
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Residues in contact with GLU 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A SER* 3.6 6.7 + - - +
56A VAL* 1.3 80.2 - - - +
58A ARG* 1.3 58.0 + - - +
60A VAL* 3.4 3.8 + - - +
61A VAL* 3.0 32.4 + - + +
140A VAL* 3.8 38.9 - - + +
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Residues in contact with ARG 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ARG* 6.6 0.2 - - - -
24A ASP* 2.8 42.9 + - - +
26A GLY 3.6 12.5 + - - -
27A THR 3.4 3.1 - - - -
28A MET 3.4 17.2 - - - +
29A THR* 3.5 6.3 + - - -
51A LEU* 3.9 20.6 - - + +
55A SER* 3.1 25.2 + - - +
57A GLU* 1.3 74.7 - - - +
59A ALA* 1.3 66.1 + - - +
61A VAL* 3.2 14.7 + - - +
62A GLU* 2.9 47.1 + - - +
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A ALA* 3.5 32.4 - - - +
51A LEU* 3.8 17.3 - - + +
52A ALA* 3.9 7.0 - - - +
55A SER 2.9 17.0 + - - +
56A VAL* 3.2 5.6 + - - +
58A ARG* 1.3 75.7 - - - +
60A VAL* 1.3 62.6 + - - +
62A GLU* 3.2 12.0 + - - +
63A LEU* 3.4 11.1 + - - +
126A ILE* 3.8 18.6 - - + -
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Residues in contact with VAL 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A VAL* 3.0 21.2 + - + +
57A GLU* 3.6 6.5 - - - +
59A ALA* 1.3 73.2 - - - +
61A VAL* 1.3 68.0 + - + +
63A LEU* 3.2 5.5 + - - +
64A ASP* 2.9 24.7 + - - +
126A ILE* 4.2 24.0 - - + -
140A VAL* 4.3 18.8 - - + +
141A ALA* 4.6 2.2 - - - -
144A PHE* 3.6 29.3 - - + -
147A ARG* 3.3 29.4 - - - +
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Residues in contact with VAL 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLY 4.8 0.7 - - - +
27A THR* 3.9 31.2 - - + +
57A GLU* 3.0 22.9 + - + +
58A ARG* 3.2 28.7 + - - +
60A VAL* 1.3 78.0 - - + +
62A GLU* 1.3 62.9 + - - +
64A ASP* 3.2 9.6 + - + +
65A THR* 2.9 29.4 + - - +
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Residues in contact with GLU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR 4.4 3.4 - - - -
28A MET* 4.1 0.7 - - - -
29A THR* 2.9 47.7 + - - +
39A MET* 3.2 30.7 - - + +
44A ALA* 3.8 27.2 - - + +
47A VAL* 4.1 10.7 - - + +
48A ALA* 4.5 3.8 - - + +
51A LEU* 4.1 7.1 - - + +
58A ARG* 2.9 35.3 + - - +
59A ALA 3.5 9.6 - - - +
60A VAL 3.2 0.4 - - - -
61A VAL* 1.3 77.4 - - - +
63A LEU* 1.3 62.3 + - - +
65A THR 3.3 0.3 + - - -
66A LEU* 3.1 18.7 + - - +
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Residues in contact with LEU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA* 4.2 11.9 - - + +
45A ALA* 4.3 10.1 - - - -
48A ALA* 3.9 23.3 - - + -
59A ALA 3.4 3.1 + - - +
60A VAL 3.2 4.9 + - - +
62A GLU* 1.3 73.7 - - - +
64A ASP* 1.3 60.9 + - - +
66A LEU* 3.4 14.7 + - + +
67A LEU* 2.8 38.5 + - + +
119A HIS* 4.7 10.3 - - + +
122A ALA* 4.3 7.4 - - + -
123A VAL* 3.9 25.8 - - + -
126A ILE* 3.7 24.7 - - + -
144A PHE* 3.8 21.8 - - + -
152A LEU* 6.5 0.2 - - + -
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Residues in contact with ASP 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A VAL* 2.9 22.8 + - - +
61A VAL* 3.2 9.8 + - + +
63A LEU* 1.3 75.2 - - - +
65A THR* 1.3 58.3 + - - +
67A LEU 3.3 0.2 + - - -
68A SER* 2.8 27.7 + - - -
144A PHE* 4.1 2.9 - - - -
147A ARG* 2.6 41.3 + - - -
148A ARG* 2.7 50.5 + - - +
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Residues in contact with THR 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR* 2.7 41.3 + - - +
28A MET* 4.1 14.1 - - + -
39A MET* 4.0 15.2 - - + +
61A VAL* 2.9 15.6 + - - +
62A GLU 3.6 4.5 - - - -
64A ASP* 1.3 76.2 - - - +
66A LEU* 1.3 61.7 + - - +
68A SER* 2.7 24.3 + - - -
69A ALA* 3.6 6.2 + - - +
80A VAL* 5.1 1.0 - - + +
108A ARG* 3.7 26.3 + - - +
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Residues in contact with LEU 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A MET* 3.8 18.5 - - + -
41A SER* 4.0 23.8 - - - +
44A ALA* 4.3 7.4 - - + -
62A GLU 3.1 11.1 + - - +
63A LEU* 3.7 14.4 - - + +
65A THR* 1.3 80.1 - - - +
67A LEU* 1.3 59.6 + - + +
69A ALA* 2.9 24.8 + - - +
70A GLN* 3.6 3.8 + - - -
76A ILE* 3.6 29.5 - - + +
77A PRO* 4.4 1.3 - - + +
80A VAL* 4.0 20.6 - - + -
119A HIS* 3.4 38.8 - - + +
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Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 2.8 27.6 + - + +
66A LEU* 1.3 75.8 - - + +
68A SER* 1.3 63.2 + - - +
70A GLN* 3.1 28.8 + - - +
76A ILE* 3.7 30.3 - - + -
119A HIS* 6.3 0.2 - - + -
144A PHE* 4.2 12.3 - - + -
148A ARG* 3.8 54.1 + - + +
151A ASP* 4.3 17.6 - - + +
152A LEU* 4.2 21.3 - - + -
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Residues in contact with SER 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ASP 2.8 15.1 + - - -
65A THR* 2.7 22.9 + - - -
66A LEU 3.2 0.2 - - - -
67A LEU* 1.3 75.4 - - - +
69A ALA* 1.3 56.3 + - - +
70A GLN 3.3 3.0 + - - +
105A PRO* 4.3 7.8 - - - +
106A ARG 5.6 0.7 - - - +
108A ARG* 3.5 29.3 + - - +
148A ARG* 4.1 13.8 - - - +
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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