Contacts of the helix formed by residues 52 - 60 (chain A) in PDB entry 1C06
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 52 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR* 4.2 11.7 + - + +
21A GLY 3.2 25.8 + - - -
22A VAL* 4.3 23.5 - - + +
23A ASN 5.1 1.0 - - - +
26A GLN* 4.7 15.9 + - - +
48A LEU 3.5 1.9 + - - +
49A LEU* 2.7 35.6 + - + +
50A GLU 2.6 4.9 + - - -
51A SER* 1.3 71.8 - - - +
53A LEU* 1.3 69.2 + - - +
54A ASP* 3.1 32.0 + - - +
55A ASN* 2.8 20.5 + - + +
56A LEU* 3.2 9.4 + - - +
70A ARG* 4.4 14.6 - - - +
88A PRO* 3.3 30.6 + - - +
89A SER* 4.2 7.9 - - - +
90A TYR 4.7 2.9 - - - -
91A ARG* 5.7 0.6 - - - +
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Residues in contact with LEU 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 SER 2.8 12.2 + - - +
52A ARG* 1.3 70.0 - - - +
54A ASP* 1.3 63.0 + - - +
56A LEU* 3.5 6.3 + - - +
57A VAL* 3.1 27.1 + - + +
73A VAL* 4.2 12.8 - - + -
78A ILE* 5.0 7.6 - - + -
80A VAL* 3.9 20.2 - - + -
85A VAL* 4.1 12.6 - - + +
87A ILE 3.5 22.2 - - - +
88A PRO* 3.8 9.0 + - + +
90A TYR* 2.9 41.3 - - + +
91A ARG* 3.7 5.2 - - - +
92A VAL* 3.7 21.3 - - + -
98A ILE* 5.1 4.4 - - + +
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Residues in contact with ASP 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 5.0 8.8 - - - +
52A ARG* 2.9 49.1 + - - +
53A LEU* 1.3 75.3 - - - +
55A ASN* 1.3 81.4 + - - +
57A VAL* 2.9 6.2 + - - +
58A TYR* 2.8 21.3 + - - +
66A ARG* 5.8 6.5 - - + +
69A ALA* 3.5 18.5 - - + +
70A ARG* 4.2 27.6 - - + -
73A VAL* 4.3 8.6 - - + +
88A PRO* 4.0 7.1 - - + +
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Residues in contact with ASN 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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20A TYR* 3.3 26.4 - - + -
49A LEU 4.6 0.9 - - - +
50A GLU* 2.8 46.5 + - - +
52A ARG* 2.8 19.8 + - + +
54A ASP* 1.3 88.2 + - - +
56A LEU* 1.3 68.6 + - - +
58A TYR* 3.0 12.9 + - - +
59A ARG* 2.6 49.5 + - - +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 4.3 6.5 + - + +
51A SER 4.6 7.2 - - - +
52A ARG 3.2 5.9 + - - +
53A LEU* 3.7 9.0 - - - +
55A ASN* 1.3 81.4 - - - +
57A VAL* 1.3 64.7 + - - +
59A ARG* 2.9 6.3 + - - -
60A LEU* 2.8 59.7 + - + +
92A VAL* 4.5 10.5 - - + -
98A ILE* 4.0 28.7 - - + -
124A LEU* 3.8 26.2 - - + -
133A GLY 4.9 2.5 - - - +
135A TYR* 3.5 36.1 - - + -
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Residues in contact with VAL 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 LEU* 3.1 18.4 + - + +
54A ASP 2.9 6.6 + - - +
56A LEU* 1.3 77.8 - - + +
58A TYR* 1.3 62.9 + - - +
59A ARG 3.1 0.7 + - - -
60A LEU* 3.5 1.3 + - - +
61A GLY 3.4 2.4 + - - -
62A LEU* 3.1 51.9 + - + +
63A ALA* 4.4 0.9 - - + -
69A ALA* 3.8 18.4 - - + +
72A LEU* 4.0 19.1 - - + -
73A VAL* 4.2 9.6 - - + -
78A ILE* 3.9 27.4 - - + -
98A ILE* 4.7 9.0 - - + -
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Residues in contact with TYR 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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20A TYR* 6.4 1.6 - + - -
54A ASP 2.8 14.5 + - - +
55A ASN* 3.7 12.3 - - - +
57A VAL* 1.3 74.2 - - - +
59A ARG* 1.3 67.6 + - + +
61A GLY* 3.7 6.3 + - - -
63A ALA* 3.4 18.1 - - - +
64A ARG 2.9 31.2 + - - -
65A THR* 4.0 10.3 - - - +
66A ARG* 4.8 16.8 - - + +
69A ALA* 3.6 20.5 - - + +
118A ASN* 4.1 24.6 + - - -
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Residues in contact with ARG 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A TYR* 4.2 11.7 + - - -
50A GLU* 2.4 36.0 + - - -
55A ASN* 2.6 40.5 + - - +
56A LEU* 3.3 9.0 - - - +
58A TYR* 1.3 78.8 - - - +
60A LEU* 1.3 56.1 + - - +
61A GLY* 2.7 17.5 + - - -
118A ASN* 3.7 20.3 - - - +
119A TYR 4.6 7.1 - - - +
120A ILE* 4.9 3.5 - - - +
121A PRO* 3.5 37.3 - - + +
123A TYR* 5.2 1.5 + - - -
124A LEU* 4.0 10.5 - - + -
143A GLU* 5.8 4.0 + - - +
144A LEU* 4.9 3.2 - - - +
145A PRO* 5.6 3.2 - - - +
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Residues in contact with LEU 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 LEU* 2.8 49.1 + - + +
57A VAL 4.1 3.4 - - - +
59A ARG* 1.3 71.5 - - - +
61A GLY* 1.3 60.2 + - - +
62A LEU* 4.0 18.6 - - + -
98A ILE* 4.1 9.9 - - + -
114A LEU* 5.9 0.3 - - - -
117A ASN* 4.4 3.9 - - - +
120A ILE* 4.1 23.8 - - + +
124A LEU* 4.0 28.7 - - + -
125A SER 4.9 0.2 - - - +
126A PHE* 3.8 35.7 - - + -
133A GLY* 3.8 31.0 - - - -
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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