Contacts of the helix formed by residues 52 - 62 (chain A) in PDB entry 4XCS
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 CYS 52 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A PHE 4.2 0.2 + - - -
51A VAL* 1.3 78.6 - - - +
53A PRO* 1.3 69.8 - - - +
54A THR* 3.0 17.0 - - - -
55A GLU* 3.0 23.6 + - + +
56A ILE 3.9 0.9 + - - -
173B CYS* 2.1 70.7 - - + +
174B PRO* 3.4 13.0 - - - +
175B ALA* 4.4 0.8 - - - +
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Residues in contact with PRO 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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48A PHE 5.3 0.7 - - - +
51A VAL* 3.0 12.8 - - + +
52A CYS* 1.3 83.5 - - - +
54A THR* 1.3 59.8 + - + +
56A ILE* 3.2 9.9 + - + +
57A ILE* 2.9 45.2 + - + +
87A TRP* 4.4 8.5 - - + -
95A GLY 4.1 14.8 - - - +
96A GLY 4.4 6.3 - - - +
97A LEU* 4.0 16.8 - - + +
174B PRO 4.0 4.7 - - - +
176B GLY* 3.7 20.6 - - - +
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Residues in contact with THR 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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52A CYS* 3.0 23.0 - - - -
53A PRO* 1.3 78.6 - - + +
55A GLU* 1.3 60.4 + - - +
57A ILE* 3.8 13.8 - - + +
58A ALA* 2.9 26.3 + - - +
202A CPS 6.0 4.3 - - + +
173B CYS* 3.0 10.4 - - - -
174B PRO* 5.6 0.4 - - + +
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Residues in contact with GLU 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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42A PHE* 5.0 6.1 - - + -
44A TYR* 2.6 27.2 + - - +
51A VAL* 5.2 0.2 - - - +
52A CYS* 3.0 19.1 + - + +
54A THR* 1.3 82.2 + - - +
56A ILE* 1.3 63.4 + - - +
58A ALA* 3.4 7.5 + - - +
59A PHE* 3.3 30.2 + - + -
128A ARG* 2.8 38.7 + - - -
150A GLY* 3.5 12.1 - - - -
151A ARG* 2.7 44.5 + - + +
201A GOL 4.4 0.8 - - - -
173B CYS* 4.3 1.4 - - - -
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Residues in contact with ILE 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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42A PHE* 6.4 0.2 - - + -
44A TYR* 3.3 26.2 - - + +
48A PHE* 3.5 31.4 - - + -
51A VAL* 3.5 28.7 - - + -
52A CYS 4.7 1.3 - - - +
53A PRO* 3.2 6.2 + - + +
55A GLU* 1.3 75.9 - - - +
57A ILE* 1.3 59.7 + - - +
59A PHE* 3.2 7.9 + - - +
60A SER* 2.9 26.2 + - - -
75A GLY* 6.1 1.8 - - - -
97A LEU* 4.2 16.2 - - + -
100A MET* 3.9 22.4 - - - -
102A ILE* 4.7 9.1 - - + +
104A LEU* 4.7 11.0 - - + -
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Residues in contact with ILE 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 PRO* 2.9 38.1 + - + +
54A THR* 3.8 13.2 - - + +
56A ILE* 1.3 76.3 - - - +
58A ALA* 1.3 51.9 + - - +
60A SER* 3.2 6.7 + - - -
61A ASP* 2.7 56.6 + - - +
92A LYS* 3.9 33.9 - - + +
96A GLY 4.1 8.3 - - - +
97A LEU* 3.7 27.4 - - + +
100A MET* 4.1 4.3 - - + -
202A CPS 5.7 1.6 - - - +
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Residues in contact with ALA 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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54A THR 2.9 17.6 + - - +
55A GLU* 3.7 7.0 - - - +
56A ILE 3.3 0.2 - - - -
57A ILE* 1.3 75.8 - - - +
59A PHE* 1.3 61.4 + - + +
61A ASP* 3.5 8.9 + - - +
62A ARG* 3.3 28.6 + - - +
151A ARG 5.7 2.2 - - - +
153A VAL* 3.9 18.4 - - + +
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Residues in contact with PHE 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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40A VAL* 5.2 0.2 - - + -
42A PHE* 3.5 44.2 - + + -
55A GLU* 3.3 23.1 - - + +
56A ILE* 3.2 9.5 + - - +
58A ALA* 1.3 76.3 - - + +
60A SER* 1.3 65.5 + - - +
62A ARG* 3.3 3.6 + - - -
63A ALA* 3.1 23.4 + - - +
66A PHE* 3.7 38.1 - + - -
73A VAL* 4.5 13.7 - - + +
102A ILE* 4.7 5.6 - - + +
151A ARG* 3.6 29.6 - - + -
153A VAL* 3.6 24.2 - - + -
156A THR* 3.6 25.6 - - + -
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Residues in contact with SER 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 ILE 2.9 13.5 + - - -
57A ILE 3.5 7.6 - - - -
59A PHE* 1.3 76.3 - - - +
61A ASP* 1.3 66.5 + - - +
63A ALA* 3.2 9.9 + - - +
99A PRO 4.1 1.9 + - - -
100A MET* 3.3 31.1 - - - +
101A ASN* 2.8 48.1 + - - +
102A ILE* 4.2 17.1 - - - +
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Residues in contact with ASP 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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57A ILE* 2.7 41.9 + - - +
58A ALA* 3.7 8.5 - - - +
60A SER* 1.3 77.9 + - - +
62A ARG* 1.3 65.3 + - + +
63A ALA 3.6 0.7 + - - -
64A GLU* 4.7 12.0 - - - +
92A LYS* 4.6 11.6 + - - -
100A MET* 6.0 0.2 - - - +
101A ASN* 4.2 8.0 - - - +
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Residues in contact with ARG 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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58A ALA* 3.3 16.3 + - - +
59A PHE 3.3 4.4 + - - +
60A SER 3.2 0.6 - - - -
61A ASP* 1.3 84.6 - - + +
63A ALA* 1.3 65.3 + - - +
64A GLU* 3.0 5.4 - - - -
65A GLU* 2.7 61.6 + - + +
66A PHE* 3.7 6.7 + - - -
153A VAL* 3.5 36.6 - - + +
154A ASP* 3.2 29.7 + - - -
157A LEU* 3.6 10.3 - - - +
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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