Contacts of the helix formed by residues 47 - 56 (chain A) in PDB entry 3APO
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 47 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A THR 3.6 1.6 + - - -
46A ALA* 1.3 74.5 - - - +
48A SER* 1.3 66.1 + - - +
49A ARG* 3.5 10.4 + - - +
50A GLU* 3.1 35.8 + - - +
51A ILE* 2.9 24.9 + - - +
93A ARG* 4.8 0.9 - - - +
481A PRO* 5.0 7.2 - - - -
484A ARG* 5.4 7.6 - - - +
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Residues in contact with SER 48 (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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46A ALA 4.2 0.2 + - - -
47A SER* 1.3 71.8 - - - +
49A ARG* 1.3 57.2 + - - +
51A ILE* 3.1 11.7 + - - +
52A ARG* 2.9 52.9 + - - +
87A LEU 6.1 0.4 - - - -
88A LYS* 5.0 13.2 + - - +
93A ARG* 4.7 6.9 + - - +
135A GLU* 4.8 10.0 + - - -
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Residues in contact with ARG 49 (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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47A SER* 3.1 11.5 + - - +
48A SER* 1.3 78.9 - - - +
50A GLU* 1.3 57.0 + - + +
52A ARG* 3.3 18.9 + - - +
53A GLN* 2.9 47.3 + - - +
125A TYR 2.7 26.4 + - - -
126A ASP* 3.2 29.8 + - - +
128A ASP 3.1 12.9 + - - -
129A PRO* 4.2 8.8 + - - +
131A ILE* 2.8 30.8 + - - +
132A ILE* 4.2 6.7 - - - +
133A THR* 4.2 24.5 + - - +
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Residues in contact with GLU 50 (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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42A VAL* 3.9 10.7 - - + +
45A THR 4.7 0.5 - - - +
46A ALA* 3.3 16.8 - - + +
47A SER* 3.1 34.8 + - - +
49A ARG* 1.3 73.2 - - - +
51A ILE* 1.3 65.2 + - - +
53A GLN* 3.6 17.1 - - - +
54A ALA* 3.1 26.3 + - - +
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Residues in contact with ILE 51 (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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37A TYR* 4.7 6.7 - - + -
40A LEU* 3.9 15.8 - - + +
42A VAL* 3.7 26.2 - - + -
46A ALA* 3.7 14.1 - - + +
47A SER 2.9 23.4 + - - +
48A SER* 3.4 10.5 - - - +
50A GLU* 1.3 77.0 - - - +
52A ARG* 1.3 52.2 + - - +
54A ALA* 3.7 3.2 - - - +
55A PHE* 2.8 36.0 + - - +
84A TYR* 3.7 24.5 - - + -
87A LEU* 4.2 32.5 - - + +
88A LYS* 4.7 5.2 - - - +
93A ARG* 4.7 8.7 - - - +
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Residues in contact with ARG 52 (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 SER* 2.9 29.1 + - - +
49A ARG* 3.5 22.1 - - - +
51A ILE* 1.3 71.7 - - - +
53A GLN* 1.3 56.7 + - - +
54A ALA 3.0 1.8 - - - -
55A PHE* 2.8 8.7 + - - +
56A LYS* 2.7 35.7 + - - +
84A TYR* 3.3 30.8 + - + +
88A LYS* 5.9 4.9 - - - +
122A PHE* 3.6 18.6 - - + -
123A GLY* 4.6 6.6 - - - +
126A ASP* 3.3 30.9 + - - +
133A THR* 4.5 14.8 + - - +
135A GLU* 4.9 13.3 + - - -
188A ASP* 4.6 12.1 + - - -
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Residues in contact with GLN 53 (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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49A ARG* 2.9 55.1 + - - +
50A GLU* 3.5 18.3 - - - +
51A ILE 3.6 0.2 - - - -
52A ARG* 1.3 72.2 - - - +
54A ALA* 1.3 58.1 - - - +
56A LYS* 3.9 14.9 - - - +
57A LYS* 3.5 23.2 + - - -
126A ASP* 3.3 41.6 + - + +
127A ASP* 4.3 7.7 - - + +
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Residues in contact with ALA 54 (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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40A LEU* 3.9 28.7 - - + +
41A GLY 5.6 0.2 - - - -
42A VAL* 4.0 16.4 - - + -
50A GLU 3.1 19.0 + - - +
51A ILE* 3.9 2.7 - - - +
52A ARG 3.0 0.6 - - - -
53A GLN* 1.3 77.2 - - - +
55A PHE* 1.3 64.5 + - - +
56A LYS 3.3 0.4 - - - -
57A LYS* 3.3 23.8 - - - +
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Residues in contact with PHE 55 (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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40A LEU* 4.7 16.1 - - + +
51A ILE 2.8 19.6 + - - +
52A ARG 3.4 2.9 - - - +
54A ALA* 1.3 78.2 - - - +
56A LYS* 1.3 50.8 + - - +
57A LYS* 2.6 23.0 + - - +
81A ASN* 3.7 36.1 - - + -
84A TYR* 3.3 54.3 - + + -
118A TYR* 3.9 33.0 - + - -
122A PHE* 3.5 23.3 - + - -
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Residues in contact with LYS 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 ARG 2.7 19.0 + - - +
53A GLN* 3.9 8.2 - - - +
54A ALA 3.3 0.4 - - - -
55A PHE* 1.3 68.2 - - - +
57A LYS* 1.3 76.2 + - - +
118A TYR* 3.4 30.1 + - + +
119A ARG* 5.2 6.0 + - - +
122A PHE* 3.3 45.3 - - + +
123A GLY 4.0 12.3 - - - -
126A ASP* 4.9 9.0 - - - -
127A ASP* 5.7 7.8 - - - +
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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