Contacts of the helix formed by residues 104 - 114 (chain A) in PDB entry 3CJD
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 HIS 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLU* 5.7 0.6 + - - -
69A ARG* 3.3 32.2 + - - +
100A PHE* 2.8 56.4 + + + +
101A ALA 3.8 3.4 - - - -
103A GLU* 1.3 92.6 + - + +
105A PRO* 1.3 58.4 - - - +
106A LYS 3.3 2.4 + - - -
107A LEU* 3.5 12.0 + - + +
108A TRP* 2.9 27.5 + - - +
202A CL 3.4 11.9 - - + -
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Residues in contact with PRO 105 (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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101A ALA 3.3 15.9 - - - +
102A ARG* 3.6 11.2 - - - +
103A GLU 3.3 10.5 - - - +
104A HIS* 1.3 85.8 - - - +
106A LYS* 1.3 71.5 + - + +
108A TRP* 3.7 4.6 - - + +
109A ARG* 3.0 35.4 + - - +
202A CL 3.9 4.7 - - + -
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Residues in contact with LYS 106 (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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24A ILE* 3.2 32.9 - - - +
25A GLU 3.4 11.1 + - - +
26A ALA 2.6 27.9 + - - -
27A GLU* 3.9 5.8 - - - +
28A GLY* 3.7 17.0 - - - +
29A LEU* 5.2 2.1 + - - +
105A PRO* 1.3 85.4 - - + +
107A LEU* 1.3 62.2 + - - +
109A ARG* 3.5 5.4 + - - +
110A ALA* 3.0 26.9 + - - +
202A CL 3.2 9.0 - - + +
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Residues in contact with LEU 107 (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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21A GLU* 4.1 9.2 - - + +
24A ILE* 3.9 16.8 - - + -
25A GLU* 3.7 29.8 - - + +
62A VAL* 3.9 28.5 - - + -
63A ASN* 4.5 0.2 - - - +
66A THR* 3.8 23.7 + - + +
69A ARG* 3.7 33.0 - - - +
104A HIS* 4.1 15.5 - - + +
106A LYS* 1.3 74.8 - - - +
108A TRP* 1.3 64.2 + - - +
110A ALA* 3.3 12.7 + - + +
111A LEU* 3.4 14.4 + - - +
202A CL 3.2 14.3 - - + +
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Residues in contact with TRP 108 (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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66A THR* 4.6 0.4 - - - +
97A TYR* 3.0 29.9 + + - -
100A PHE* 4.2 22.2 - + + -
101A ALA* 3.5 37.7 - - + +
104A HIS 2.9 19.8 + - - +
105A PRO* 3.7 13.2 - - + +
107A LEU* 1.3 76.8 - - - +
109A ARG* 1.3 82.8 + - + +
111A LEU* 3.1 28.4 + - + +
112A PHE* 3.5 19.0 - + - -
165A HIS* 3.6 25.8 - + - -
168A VAL* 4.0 20.9 - - + -
169A LEU* 4.0 26.2 - - + -
172A LEU* 4.3 11.7 - - + -
173A GLU* 6.2 1.3 - - + -
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Residues in contact with ARG 109 (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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29A LEU* 6.0 0.2 - - - -
105A PRO 3.0 23.1 + - - +
106A LYS* 3.9 5.8 - - - +
108A TRP* 1.3 99.7 - - + +
110A ALA* 1.3 57.6 + - - +
112A PHE* 3.1 10.9 + - - +
113A ASP* 3.0 60.4 + - - +
165A HIS* 6.5 0.2 - - - -
169A LEU* 4.4 11.7 - - - +
173A GLU* 3.0 34.5 + - - +
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Residues in contact with ALA 110 (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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24A ILE* 4.1 18.2 - - + -
29A LEU* 4.2 24.4 - - + +
59A THR* 4.5 5.8 - - + -
62A VAL* 5.8 0.2 - - + -
63A ASN* 3.2 25.9 + - - +
106A LYS 3.0 14.1 + - - +
107A LEU* 3.5 11.9 - - + +
108A TRP 3.3 0.6 - - - -
109A ARG* 1.3 75.6 - - - +
111A LEU* 1.3 62.3 + - - +
112A PHE 3.2 0.2 - - - -
113A ASP* 4.6 0.4 - - - -
114A VAL* 3.2 17.8 + - - +
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Residues in contact with LEU 111 (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 ASN* 3.6 37.6 + - + +
66A THR* 3.8 28.9 - - + -
67A PHE* 4.0 19.3 - - + -
70A LEU* 4.7 12.6 - - + -
97A TYR* 5.9 0.2 - - + -
100A PHE* 5.1 0.9 - - + -
107A LEU 3.4 6.3 + - - +
108A TRP* 3.1 23.7 + - + +
110A ALA* 1.3 78.0 - - - +
112A PHE* 1.3 69.0 + - + +
114A VAL* 3.8 5.9 - - - +
126A TYR* 4.5 2.5 + - - +
203A STE 3.2 43.5 - - + +
175B ARG* 3.2 8.3 + - - -
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Residues in contact with PHE 112 (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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97A TYR* 3.2 27.4 - - - -
108A TRP* 3.5 29.6 - + - -
109A ARG* 3.1 12.1 + - - +
111A LEU* 1.3 79.2 - - + +
113A ASP* 1.3 64.2 + - - +
114A VAL 3.7 0.4 - - - -
161A PHE* 3.9 5.6 - + - -
165A HIS* 3.3 33.0 - + - +
203A STE 3.3 41.7 - - + -
170B LEU* 3.8 23.8 - - + -
173B GLU* 4.8 5.7 - - - +
175B ARG* 3.2 28.6 + - - +
177B SER* 4.1 6.1 - - - -
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Residues in contact with ASP 113 (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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29A LEU* 4.0 20.5 - - + +
109A ARG* 3.0 53.7 + - - +
110A ALA 3.6 0.2 + - - -
112A PHE* 1.3 82.9 - - - +
114A VAL* 1.3 64.8 + - - +
115A GLU* 3.9 3.1 + - - +
175B ARG* 5.1 0.2 - - - -
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Residues in contact with VAL 114 (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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29A LEU* 3.8 7.3 - - + +
56A ASN* 3.2 24.2 - - - +
59A THR* 3.7 23.1 - - + -
60A LEU* 3.7 22.9 - - + -
63A ASN* 3.3 19.3 - - - +
110A ALA 3.2 14.9 + - - +
111A LEU 3.8 11.9 - - - +
113A ASP* 1.3 80.3 - - - +
115A GLU* 1.3 56.7 + - - +
116A MSE 3.1 21.5 + - + -
126A TYR* 4.2 2.0 - - - +
175B ARG* 3.2 19.6 + - - +
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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