Contacts of the helix formed by residues 116 - 128 (chain C) in PDB entry 4QYJ
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 116 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C LEU* 3.5 30.1 - - + +
90C GLU* 4.4 8.1 - - + -
93C GLY* 3.6 26.9 - - - +
96C LEU* 3.9 23.1 - - + -
97C ALA* 4.0 6.1 - - + +
111C SER 2.9 18.8 + - - +
112C LYS* 3.8 9.9 - - - +
115C GLU* 1.3 78.8 - - + +
117C GLY* 1.3 58.7 + - - +
118C ALA 3.6 0.2 - - - -
119C SER* 3.8 2.0 - - - -
120C ALA* 3.4 23.4 + - - +
172C LEU* 4.1 9.0 - - + -
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Residues in contact with GLY 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C GLU* 5.0 9.0 - - - +
112C LYS 3.5 11.5 + - - -
113C LEU* 3.7 11.9 + - - -
116C VAL* 1.3 82.1 - - - +
118C ALA* 1.3 61.1 + - - +
119C SER 3.2 1.3 - - - -
120C ALA* 3.8 5.6 + - - +
121C GLN* 3.6 17.8 + - - +
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Residues in contact with ALA 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C LEU 3.4 9.1 + - - +
114C MET* 3.9 24.5 - - + +
117C GLY* 1.3 75.8 - - - +
119C SER* 1.3 59.2 + - - +
121C GLN* 3.2 17.6 - - - +
122C TRP* 3.1 40.3 + - + -
173C LEU* 3.6 11.7 - - + -
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Residues in contact with SER 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C LEU* 4.0 11.2 - - - -
115C GLU 2.4 26.8 + - - -
116C VAL 3.8 4.5 - - - -
118C ALA* 1.3 77.3 - - - +
120C ALA* 1.3 62.4 + - - +
123C LEU* 3.4 21.1 + - - +
172C LEU* 3.6 5.6 - - - +
173C LEU* 3.2 29.6 - - - +
176C VAL* 3.5 27.4 - - - +
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Residues in contact with ALA 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA* 3.5 33.7 - - - +
89C LEU* 4.5 4.7 - - + +
90C GLU* 4.1 15.0 - - + +
116C VAL 3.4 15.5 + - - +
117C GLY 4.1 4.0 - - - +
118C ALA 3.3 0.4 - - - -
119C SER* 1.3 79.3 - - - +
121C GLN* 1.3 59.5 + - - +
123C LEU* 3.5 1.3 + - - -
124C ARG* 3.3 40.9 + - - +
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Residues in contact with GLN 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A SER* 4.3 28.1 + - - +
79A GLU* 5.0 3.0 - - - +
117C GLY 3.6 11.1 + - - +
118C ALA* 3.2 23.0 - - - +
120C ALA* 1.3 75.0 - - - +
122C TRP* 1.3 63.2 + - - +
124C ARG* 3.7 7.6 + - - +
125C TYR* 3.2 26.2 + - - +
461C ASP* 4.3 9.1 + - - -
462C PRO* 3.7 29.2 - - + +
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Residues in contact with TRP 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ALA* 3.1 34.8 + - + +
119C SER* 3.9 0.4 - - - +
120C ALA 3.4 0.2 - - - -
121C GLN* 1.3 80.7 - - - +
123C LEU* 1.3 64.8 + - - +
125C TYR* 3.7 1.0 + - - +
126C MET* 3.2 45.7 + - + +
173C LEU* 4.3 4.9 - - + -
176C VAL* 3.7 24.9 - - + -
177C TRP* 3.2 56.8 + + - +
180C ALA* 4.3 2.2 - - + +
460C VAL* 4.1 15.3 - - + -
461C ASP* 3.2 32.5 - - - -
462C PRO* 3.7 33.6 + - + +
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Residues in contact with LEU 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C LEU* 3.8 34.0 - - + +
85C LEU* 4.1 14.6 - - + +
86C ALA* 3.9 20.2 - - + +
89C LEU* 3.9 23.6 - - + -
119C SER 3.4 17.6 + - - +
120C ALA 3.8 4.5 - - - +
121C GLN 3.3 0.2 - - - -
122C TRP* 1.3 75.4 - - - +
124C ARG* 1.3 68.0 + - - +
126C MET* 2.9 3.1 + - - +
127C ALA* 2.8 26.1 + - - +
176C VAL* 4.0 11.0 - - + -
179C ILE* 4.5 11.4 - - + -
180C ALA* 3.8 23.1 - - + -
204C LEU* 5.5 0.7 - - + -
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Residues in contact with ARG 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 3.6 23.8 - - - +
80A ARG* 3.3 25.0 - - - +
83A LEU* 3.6 21.4 - - - +
128A GLY* 6.0 0.5 - - - -
132A LYS* 5.1 0.2 + - - -
83C LEU* 3.8 23.3 + - + +
86C ALA* 3.7 26.3 + - + +
87C ASP* 3.2 30.5 + - - -
90C GLU* 3.2 36.8 + - - -
120C ALA* 3.3 18.9 + - - +
121C GLN* 4.0 6.1 - - - +
123C LEU* 1.3 79.1 - - - +
125C TYR* 1.3 62.8 + - - +
127C ALA* 3.1 13.2 + - - +
128C GLY* 3.3 6.2 + - - -
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Residues in contact with TYR 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A GLU* 3.9 9.4 + - - +
131A THR* 3.4 37.2 - - + -
132A LYS* 2.9 32.0 + - - +
121C GLN 3.2 16.8 + - - +
122C TRP 3.9 2.5 - - - +
124C ARG* 1.3 77.4 - - - +
126C MET* 1.3 78.3 + - + +
128C GLY 3.9 0.5 + - - -
129C TRP* 3.5 33.5 + + - -
461C ASP* 5.7 0.4 - - - -
462C PRO* 3.3 37.2 + - + -
463C ASN* 2.3 44.0 + - + -
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Residues in contact with MET 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C LEU* 4.5 0.4 - - + -
122C TRP* 3.2 30.9 + - + +
123C LEU 2.9 3.5 + - - +
125C TYR* 1.3 97.3 - - + +
127C ALA* 1.3 64.3 + - - +
128C GLY 3.2 0.4 - - - -
129C TRP* 3.2 25.8 + - + +
180C ALA* 4.0 18.2 - - + +
181C PRO* 4.0 37.7 - - + -
184C ALA* 3.2 20.8 - - - +
462C PRO 4.2 8.7 - - - +
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Residues in contact with ALA 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C GLU* 3.3 27.0 - - - +
82C LEU* 3.6 34.5 - - + +
83C LEU* 4.3 10.3 - - + +
123C LEU 2.8 17.2 + - - +
124C ARG* 3.1 9.2 + - - +
126C MET* 1.3 78.0 - - - +
128C GLY* 1.3 55.3 + - - +
129C TRP 3.2 0.4 - - - -
130C ALA* 3.3 20.6 - - - +
131C THR 4.6 0.5 + - - -
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Residues in contact with GLY 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ARG 6.1 0.2 - - - -
128A GLY* 4.2 10.8 - - - +
132A LYS* 4.2 15.3 - - - -
79C GLU* 5.0 4.0 - - - -
83C LEU* 5.9 0.2 - - - +
124C ARG 3.3 8.4 + - - -
125C TYR 3.9 0.2 + - - -
126C MET 3.2 0.6 - - - -
127C ALA* 1.3 77.1 - - - +
129C TRP* 1.3 58.1 + - - +
130C ALA 3.3 1.1 - - - -
131C THR* 4.4 2.9 - - - -
132C LYS* 2.8 40.4 + - - +
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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