Contacts of the helix formed by residues 120 - 130 (chain D) in PDB entry 4QPL
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 VAL 120 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75D HIS 3.7 11.4 - - - +
76D PRO 3.0 8.4 + - - +
78D ILE 3.6 26.0 - - - +
79D ASN* 3.8 18.2 - - + -
118D PRO 4.2 1.8 - - - -
119D LEU* 1.3 79.2 - - - +
121D PRO* 1.3 69.9 - - + +
122D ASP* 4.6 4.7 - - + +
123D ILE* 3.1 31.7 + - + +
124D ALA* 2.9 20.8 + - - +
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Residues in contact with PRO 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D PRO* 3.7 16.6 - - + +
119D LEU 3.4 11.4 - - - +
120D VAL* 1.3 84.5 - - + +
122D ASP* 1.3 63.2 + - - +
124D ALA* 3.1 8.8 + - + +
125D GLN* 2.8 31.9 + - - +
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Residues in contact with ASP 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D VAL* 3.3 5.0 + - + +
121D PRO* 1.3 81.5 - - - +
123D ILE* 1.3 65.0 + - + +
125D GLN* 3.5 6.0 + - - +
126D ILE* 3.3 30.3 + - + +
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Residues in contact with ILE 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D ILE 5.4 1.1 - - - +
74D TYR* 3.6 48.5 - - + +
75D HIS 3.7 17.3 - - - +
76D PRO* 3.5 27.8 - - + -
78D ILE 5.4 0.7 - - - +
120D VAL* 3.1 31.6 + - + +
122D ASP* 1.3 77.3 - - + +
124D ALA* 1.3 64.9 + - - +
126D ILE* 3.1 4.6 + - - +
127D TYR* 2.9 21.0 + - - +
134D TYR* 3.8 15.4 - - + -
141D TRP* 5.4 4.7 - - + -
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Residues in contact with ALA 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76D PRO* 3.7 19.0 - - + +
115D PRO* 4.0 12.2 - - + +
118D PRO* 3.5 30.7 - - + -
120D VAL 2.9 9.0 + - - +
121D PRO 3.5 8.1 - - - +
123D ILE* 1.3 76.1 - - - +
125D GLN* 1.3 62.5 + - - +
127D TYR* 3.3 6.5 + - - +
128D LYS* 3.2 31.3 + - - +
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Residues in contact with GLN 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121D PRO 2.8 16.7 + - - +
122D ASP* 3.8 7.6 - - - +
124D ALA* 1.3 75.4 - - - +
126D ILE* 1.3 58.5 + - + +
128D LYS* 3.3 23.8 + - - +
129D SER* 2.9 52.9 + - - +
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Residues in contact with ILE 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D TYR* 3.4 22.7 - - - +
122D ASP* 3.3 17.9 + - + +
123D ILE* 3.1 8.2 + - + +
125D GLN* 1.3 75.2 - - + +
127D TYR* 1.3 60.1 + - - +
129D SER* 4.4 3.1 - - - +
130D ASP* 2.7 48.8 + - + +
133D LYS* 3.9 32.1 - - + +
134D TYR* 3.8 20.0 - - + +
137D HIS* 4.6 2.7 - - + +
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Residues in contact with TYR 127 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76D PRO* 4.8 3.6 - - + -
111D CYS 5.4 0.2 + - - -
112D ASP* 4.7 6.6 + - - +
113D PRO* 3.6 42.6 + - + +
115D PRO* 3.9 35.4 - - + -
123D ILE 2.9 12.5 + - - +
124D ALA* 3.4 11.4 - - - +
126D ILE* 1.3 78.5 - - - +
128D LYS* 1.3 64.0 + - - +
131D LYS* 3.1 58.5 + - + +
134D TYR* 3.6 44.6 - + + +
135D ASN* 5.8 0.2 - - - -
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Residues in contact with LYS 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115D PRO* 3.7 42.4 + - + -
116D ASP* 3.9 16.7 + - - +
118D PRO* 6.1 1.2 - - - +
124D ALA* 3.2 16.9 + - - +
125D GLN* 3.7 22.9 + - - +
127D TYR* 1.3 81.4 - - + +
129D SER* 1.3 62.8 + - - +
131D LYS 5.4 0.2 + - - -
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Residues in contact with SER 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D GLN* 2.9 36.7 + - - +
126D ILE* 4.2 2.5 - - - -
128D LYS* 1.3 76.9 - - - +
130D ASP* 1.3 63.6 + - - +
131D LYS 4.0 1.1 - - - -
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Residues in contact with ASP 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D ILE* 2.7 22.2 + - + +
129D SER* 1.3 78.9 - - - +
131D LYS* 1.3 61.4 + - - +
132D GLU* 3.8 10.1 + - - +
133D LYS* 3.2 40.7 + - + +
134D TYR 2.9 23.6 + - - -
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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