Contacts of the helix formed by residues 56 - 69 (chain A) in PDB entry 4RTL
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 ASN 56 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A TRP* 4.4 12.6 - - + -
54A ASP* 3.2 15.5 + - - +
55A ILE* 1.3 77.0 - - + +
57A SER* 1.3 61.2 + - - +
58A ASP* 3.1 22.0 + - - +
59A LEU* 3.1 28.4 + - + +
60A ILE* 3.4 18.2 + - - +
111A PHE* 5.4 2.0 - - - -
123A CYS* 4.2 16.2 - - - -
125A TYR* 4.0 20.7 + - - -
162A CYS* 4.3 1.6 - - - -
301A SFG 4.4 6.0 + - - +
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Residues in contact with SER 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 ILE 3.5 4.2 + - - -
56A ASN* 1.3 70.9 + - - +
58A ASP* 1.3 71.9 + - - +
60A ILE* 4.1 4.0 - - - +
61A SER* 3.3 24.3 + - - -
162A CYS* 3.7 23.6 - - - -
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Residues in contact with ASP 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASN* 3.1 8.7 + - - +
57A SER* 1.3 82.5 + - - +
59A LEU* 1.3 60.7 + - - +
61A SER* 4.0 4.3 - - - -
62A LEU* 3.3 23.0 + - - +
98A PHE* 4.2 9.7 - - + -
107A ARG* 3.3 31.7 + - - -
111A PHE* 4.1 20.2 - - + -
125A TYR* 3.1 32.3 + - - +
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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
----------------------------------------------------------
8A LEU* 4.0 20.0 - - + -
10A TRP* 4.3 26.2 - - + -
36A VAL* 4.9 1.1 - - + -
37A GLY* 3.9 17.7 - - - +
54A ASP* 4.1 32.5 - - + +
56A ASN* 3.1 21.3 + - + +
57A SER 3.2 0.2 - - - -
58A ASP* 1.3 74.7 - - - +
60A ILE* 1.3 66.3 + - + +
62A LEU* 3.4 11.0 + - + +
63A TYR* 3.2 57.0 + - + +
111A PHE* 5.1 7.1 - - + -
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Residues in contact with ILE 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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36A VAL* 5.0 4.0 - - + -
52A LEU 4.8 2.0 - - - +
53A ALA* 4.6 4.0 - - - -
54A ASP* 4.2 21.8 - - + +
56A ASN 3.4 16.6 + - - +
57A SER 4.3 3.6 - - - +
58A ASP 3.5 0.2 - - - -
59A LEU* 1.3 77.9 - - + +
61A SER* 1.3 61.5 + - - +
63A TYR* 3.4 11.9 + - + +
64A ASN* 3.3 33.4 + - - +
160A PHE* 4.3 21.5 - - + +
161A TYR* 3.6 29.2 - - - +
162A CYS* 4.2 26.7 - - + +
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Residues in contact with SER 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A SER 3.3 17.0 + - - -
58A ASP* 4.0 5.4 - - - -
59A LEU 3.3 0.2 - - - -
60A ILE* 1.3 78.0 - - - +
62A LEU* 1.3 62.5 + - - +
64A ASN* 3.4 11.2 + - - +
65A ILE* 3.3 27.4 + - - +
104A PRO* 4.5 20.4 + - - +
108A ALA* 5.6 0.9 - - - +
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Residues in contact with LEU 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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7A PHE* 4.3 15.0 - - + -
8A LEU* 4.2 23.1 - - + -
58A ASP 3.3 12.8 + - - +
59A LEU* 3.6 12.6 - - + +
60A ILE 3.4 0.2 - - - -
61A SER* 1.3 80.1 - - - +
63A TYR* 1.3 66.9 + - + +
65A ILE* 3.5 2.4 + - - +
66A VAL* 3.2 36.2 + - + +
73A TYR* 3.6 25.1 - - + +
108A ALA* 3.9 32.1 - - + +
111A PHE* 4.1 25.1 - - + -
112A LEU* 5.8 2.7 - - + +
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Residues in contact with TYR 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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7A PHE* 4.1 21.8 - + - -
8A LEU* 4.3 6.4 - - + +
36A VAL* 4.7 11.4 - - + -
37A GLY 2.9 27.5 + - - -
38A ALA* 3.5 18.7 + - - -
39A GLY* 6.0 0.4 - - - -
59A LEU* 3.2 40.3 + - + +
60A ILE* 3.7 13.5 - - + +
61A SER 3.3 0.2 - - - -
62A LEU* 1.3 82.3 - - + +
64A ASN* 1.3 62.9 + - - +
66A VAL* 3.7 4.3 + - + +
67A LYS* 3.3 23.2 + - - +
151A PHE* 3.6 35.0 - + + -
160A PHE* 3.7 43.2 - + + -
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Residues in contact with ASN 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 ILE* 3.3 28.4 + - - +
61A SER* 3.7 10.8 - - - +
62A LEU 3.3 0.2 - - - -
63A TYR* 1.3 77.0 - - - +
65A ILE* 1.3 66.6 + - + +
67A LYS* 3.5 6.9 + - - +
68A MET* 3.2 48.7 + - + +
160A PHE* 4.3 22.3 + - - +
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Residues in contact with ILE 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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61A SER* 3.3 18.5 + - - +
62A LEU 3.5 6.5 + - - +
64A ASN* 1.3 75.6 - - + +
66A VAL* 1.3 65.9 + - + +
68A MET* 4.9 7.0 - - + -
69A ARG* 3.0 52.2 + - + +
73A TYR* 4.1 21.3 - - + +
104A PRO* 4.6 11.2 - - + +
105A PHE* 4.0 35.2 - - + +
108A ALA* 4.4 16.6 - - + -
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Residues in contact with VAL 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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7A PHE* 4.7 5.4 - - + -
62A LEU* 3.2 29.3 + - + +
63A TYR* 4.1 6.1 - - - +
65A ILE* 1.3 78.1 - - + +
67A LYS* 1.3 57.6 + - - +
70A THR* 3.1 29.4 + - + +
73A TYR* 4.1 35.0 - - + -
148A LEU* 4.5 30.5 - - + +
151A PHE* 4.3 22.2 - - + -
152A ALA* 4.0 7.4 - - + +
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Residues in contact with LYS 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 TYR 3.3 16.4 + - - +
64A ASN* 3.8 9.0 - - - +
65A ILE 3.2 0.4 - - - -
66A VAL* 1.3 82.6 - - - +
68A MET* 1.3 69.6 + - + +
70A THR* 3.7 8.0 + - - -
151A PHE* 6.0 1.1 - - + -
152A ALA* 4.9 8.6 - - - +
155A ALA* 3.2 33.4 + - + +
156A GLN* 3.9 44.6 + - - +
158A ALA 3.2 24.0 + - - -
159A PHE* 5.0 8.1 - - - -
160A PHE* 4.7 11.4 - - + -
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Residues in contact with MET 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 ASN* 3.2 41.4 + - + +
65A ILE* 4.6 7.6 - - + +
67A LYS* 1.3 90.4 - - + +
69A ARG* 1.3 71.4 + - + +
70A THR 3.8 1.5 + - - -
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Residues in contact with ARG 69 (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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65A ILE* 3.0 37.4 + - + +
68A MET* 1.3 89.6 - - + +
70A THR* 1.3 63.4 + - - +
71A ASP 3.6 1.5 + - - -
72A GLU* 3.0 45.8 + - + +
73A TYR* 3.1 22.2 + - - +
105A PHE* 3.6 37.7 - - + +
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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