Contacts of the helix formed by residues 51 - 61 (chain A) in PDB entry 4ORA
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 ARG 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A GLU 3.2 25.1 + - - -
42A GLU 3.4 15.3 + - - -
43A VAL* 2.8 19.1 + - - +
44A PHE 3.3 13.7 + - - -
45A ASP* 3.4 36.6 - - + +
46A LEU 4.6 1.0 - - - +
49A ILE 4.4 1.1 - - - +
50A PRO* 1.3 73.6 - - - +
52A VAL* 1.3 64.7 + - - +
53A ASP 3.4 2.5 - - - +
54A VAL* 3.4 23.3 + - + +
55A LEU* 3.2 20.8 + - - +
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Residues in contact with VAL 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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50A PRO 3.6 3.8 + - - -
51A ARG* 1.3 73.3 - - - +
53A ASP* 1.3 73.6 + - - +
55A LEU* 3.3 4.0 + - + +
56A LYS* 2.9 26.5 + - - +
141A TYR* 3.5 27.5 - - + +
144A VAL* 3.7 19.3 - - + -
145A LEU* 3.6 23.6 - - + -
148A LEU* 3.7 24.4 - - + +
149A TYR* 5.2 5.4 - - + +
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Residues in contact with ASP 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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51A ARG 3.4 0.2 - - - -
52A VAL* 1.3 87.5 - - - +
54A VAL* 1.3 64.6 + - + +
56A LYS* 4.0 14.7 + - - +
57A ASN* 3.0 41.7 + - - +
141A TYR* 5.1 2.9 + - - -
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Residues in contact with VAL 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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38A LEU* 4.0 23.3 - - + -
42A GLU* 3.6 21.5 - - + +
43A VAL* 4.9 2.2 - - - -
51A ARG* 3.4 31.7 + - + +
53A ASP* 1.3 79.7 - - + +
55A LEU* 1.3 63.4 + - - +
57A ASN* 4.0 5.4 - - - +
58A HIS* 3.2 22.7 + - + +
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Residues in contact with LEU 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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38A LEU* 4.6 9.2 - - + -
43A VAL* 5.1 11.7 - - + -
50A PRO* 6.5 0.2 - - + -
51A ARG 3.2 11.5 + - - +
52A VAL* 3.5 9.4 - - - +
54A VAL* 1.3 83.4 - - - +
56A LYS* 1.3 61.5 - - - +
58A HIS* 3.4 1.6 + - + +
59A LEU* 3.0 50.9 + - + +
65A VAL* 4.0 26.7 - - + -
73A ILE* 4.8 11.0 - - + -
140A LEU* 4.1 13.7 - - + +
141A TYR* 4.2 9.6 - - + -
144A VAL* 3.6 36.6 - - + -
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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 VAL 2.9 17.3 + - - +
53A ASP* 4.0 13.5 + - - +
55A LEU* 1.3 77.0 - - - +
57A ASN* 1.3 67.1 + - - +
59A LEU* 3.0 5.2 + - - +
60A VAL* 2.9 44.7 + - + +
104A PHE* 5.0 0.7 - - + -
108A MET* 3.7 36.8 - - - -
112A GLU* 4.1 21.0 + - - -
141A TYR* 3.7 26.5 - - + +
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Residues in contact with ASN 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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53A ASP* 3.0 29.4 + - - +
54A VAL* 4.0 6.2 - - - +
56A LYS* 1.3 89.0 + - - +
58A HIS* 1.3 61.4 + - - +
60A VAL* 3.8 5.9 + - - +
61A LYS* 3.3 37.3 + - + +
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Residues in contact with HIS 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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34A PRO* 3.8 21.5 - - + +
36A HIS 3.5 20.2 + - - -
38A LEU* 3.4 39.9 - - + +
54A VAL 3.2 17.2 + - - +
55A LEU 3.7 2.9 - - - +
56A LYS 3.1 0.4 - - - -
57A ASN* 1.3 79.2 - - - +
59A LEU* 1.3 61.6 + - + +
61A LYS* 3.2 18.2 + - - +
63A GLY* 2.8 32.3 + - - -
64A ARG 2.9 46.7 + - - -
65A VAL* 4.7 3.8 - - + -
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Residues in contact with LEU 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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55A LEU* 3.0 51.1 + - + +
56A LYS 3.8 0.7 - - - +
58A HIS* 1.3 76.3 - - + +
60A VAL* 1.3 61.4 + - - +
62A GLU* 2.8 21.3 + - - -
63A GLY 3.7 20.2 - - - +
65A VAL* 5.0 6.1 - - + -
104A PHE* 3.8 28.5 - - + -
105A PHE* 4.4 5.9 - - - -
137A GLU* 3.7 44.4 - - + +
140A LEU* 4.8 6.5 - - + -
141A TYR* 4.3 5.8 - - + +
179A TYR* 4.9 9.0 - - - +
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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 LYS* 2.9 45.0 + - + +
57A ASN* 4.0 7.9 - - - +
59A LEU* 1.3 75.8 - - - +
61A LYS* 1.3 61.7 + - + +
62A GLU* 3.3 4.3 + - - +
104A PHE* 4.0 12.3 - - + -
105A PHE* 3.3 34.3 - - + -
108A MET* 4.4 7.4 - - + -
349A PRO* 5.5 0.7 - - - +
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Residues in contact with LYS 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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32A PHE 5.0 2.1 - - - +
33A PRO* 3.6 7.7 - - + +
34A PRO* 3.1 37.0 - - + +
57A ASN* 3.3 29.0 + - - +
58A HIS* 3.2 13.5 + - - +
59A LEU 3.1 1.4 - - - -
60A VAL* 1.3 78.6 - - + +
62A GLU* 1.3 68.7 + - - +
63A GLY 3.2 0.2 - - - -
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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