Contacts of the helix formed by residues 116 - 128 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A LEU* 3.2 31.6 - - + +
90A GLU* 4.4 7.9 - - + -
93A GLY* 3.6 27.4 - - - +
96A LEU* 3.9 23.3 - - + -
97A ALA* 4.0 5.6 - - + +
111A SER 2.9 19.9 + - - +
112A LYS* 3.8 10.5 - - - +
115A GLU* 1.3 79.9 - - + +
117A GLY* 1.3 58.6 + - - +
119A SER* 3.8 2.0 - - - -
120A ALA* 3.4 23.0 + - - +
172A LEU* 4.1 8.7 - - + -
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLU* 5.0 9.0 - - - +
112A LYS 3.5 11.9 + - - -
113A LEU* 3.7 13.0 + - - -
116A VAL* 1.3 80.6 - - - +
118A ALA* 1.3 60.8 + - - +
119A SER 3.2 1.1 - - - -
120A ALA* 3.8 7.3 + - - +
121A GLN* 3.6 17.9 + - - +
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Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A LEU 3.4 9.3 + - - +
114A MET* 3.9 25.0 - - + +
117A GLY* 1.3 76.0 - - - +
119A SER* 1.3 55.1 + - - +
121A GLN* 3.2 18.0 - - - +
122A TRP* 2.4 45.2 + - - +
173A LEU* 3.6 10.8 - - + -
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Residues in contact with SER 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 3.8 11.2 - - - -
115A GLU 2.4 27.7 + - - -
116A VAL 3.8 4.3 - - - -
117A GLY 3.2 0.2 - - - -
118A ALA* 1.3 77.3 - - - +
120A ALA* 1.3 63.3 + - - +
123A LEU* 3.4 20.6 + - - +
172A LEU* 3.6 4.8 - - - +
173A LEU* 3.2 29.2 - - - +
176A VAL* 3.5 28.9 - - - +
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Residues in contact with ALA 120 (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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86A ALA* 3.5 31.8 - - - +
89A LEU* 4.4 4.2 - - + +
90A GLU* 4.1 15.3 - - + +
116A VAL 3.4 15.6 + - - +
117A GLY 3.8 4.5 + - - +
118A ALA 3.3 0.4 - - - -
119A SER* 1.3 79.3 - - - +
121A GLN* 1.3 60.8 + - - +
123A LEU* 3.5 1.3 + - - -
124A ARG* 3.3 40.2 + - - +
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Residues in contact with GLN 121 (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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117A GLY 3.6 10.3 + - - +
118A ALA* 3.2 26.3 + - - +
119A SER 3.2 0.2 - - - -
120A ALA* 1.3 75.6 - - - +
122A TRP* 1.3 65.5 + - - +
123A LEU 3.3 0.2 - - - -
124A ARG* 3.7 6.8 + - - +
125A TYR* 3.2 25.8 + - - +
462A PRO* 3.7 21.7 - - + +
141B SER* 3.1 29.5 + - - +
76C SER* 4.5 18.7 - - - +
79C GLU* 5.2 2.1 - - - +
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Residues in contact with TRP 122 (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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118A ALA* 2.4 50.9 + - - +
119A SER 3.6 0.2 + - - -
120A ALA 3.4 0.2 - - - -
121A GLN* 1.3 76.3 - - + +
123A LEU* 1.3 68.4 + - - +
125A TYR* 3.6 1.4 + - - +
126A MET* 3.1 38.1 + - + +
173A LEU* 4.1 7.1 - - + +
176A VAL* 3.8 18.8 - - + -
177A TRP* 3.5 34.7 - + - +
180A ALA* 4.3 3.3 - - + +
181A PRO* 6.1 2.2 - - + -
460A VAL* 4.6 8.4 + - + +
461A ASP* 3.4 25.6 - - - -
462A PRO* 3.7 33.4 - - + +
478A HIS* 2.5 61.7 - + + -
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Residues in contact with LEU 123 (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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82A LEU* 3.8 34.2 - - + +
85A LEU* 4.1 23.3 - - + -
86A ALA* 3.9 25.6 - - + +
89A LEU* 4.3 13.2 - - + -
119A SER 3.4 17.3 + - - +
120A ALA 3.8 4.9 - - - +
121A GLN 3.3 0.4 - - - -
122A TRP* 1.3 75.8 - - - +
124A ARG* 1.3 66.6 + - - +
126A MET* 2.9 3.2 + - - +
127A ALA* 2.8 25.6 + - - +
176A VAL* 4.0 11.0 - - + -
179A ILE* 4.5 8.3 - - + -
180A ALA* 3.8 22.2 - - + -
204A LEU* 5.5 0.2 - - + -
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Residues in contact with ARG 124 (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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82A LEU 5.3 0.2 - - - -
83A LEU* 4.3 11.1 + - - +
86A ALA* 3.7 25.4 + - + +
87A ASP* 3.2 30.3 + - - -
90A GLU* 3.2 36.2 + - - -
120A ALA* 3.3 18.7 + - - +
121A GLN* 4.0 6.3 - - - +
122A TRP 3.3 0.2 - - - -
123A LEU* 1.3 77.6 - - - +
125A TYR* 1.3 61.8 + - - +
127A ALA* 3.1 18.1 + - - +
128A GLY* 3.3 6.4 + - - -
79C GLU* 3.7 24.6 - - - +
80C ARG* 3.2 27.8 - - - +
83C LEU* 3.8 25.2 - - + +
128C GLY* 6.1 0.3 - - - -
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Residues in contact with TYR 125 (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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121A GLN 3.2 16.7 + - - +
122A TRP 3.8 2.5 - - - +
123A LEU 3.2 0.2 - - - -
124A ARG* 1.3 77.4 - - - +
126A MET* 1.3 77.9 + - + +
128A GLY 3.9 1.1 + - - -
129A TRP* 3.3 30.9 + + - -
461A ASP* 5.8 0.2 - - - -
462A PRO* 3.3 37.0 - - + -
463A ASN* 2.3 43.1 + - + -
479A GLY* 3.6 7.4 + - - -
79C GLU* 3.8 11.0 + - - +
131C THR* 3.4 40.4 - - + -
132C LYS* 2.9 28.4 + - - +
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Residues in contact with MET 126 (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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82A LEU* 4.5 0.7 - - + -
122A TRP* 3.1 29.3 + - + +
123A LEU 2.9 3.1 + - - +
125A TYR* 1.3 99.7 - - + +
127A ALA* 1.3 65.3 + - - +
128A GLY 3.2 0.7 - - - -
129A TRP* 3.1 25.1 + - - +
180A ALA* 4.0 18.8 - - + +
181A PRO* 4.0 34.8 - - + -
184A ALA* 3.2 20.7 - - + +
462A PRO 4.2 8.5 - - - +
478A HIS* 4.6 5.4 - - - +
479A GLY 4.2 5.6 - - - +
482A ALA* 4.1 23.1 - - + -
483A ILE* 5.0 4.0 - - - -
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 3.4 16.4 - - - +
82A LEU* 3.6 28.9 - - + +
83A LEU* 3.1 31.2 - - + -
123A LEU 2.8 17.5 + - - +
124A ARG 3.3 4.0 - - - +
126A MET* 1.3 79.0 - - - +
128A GLY* 1.3 55.1 + - - +
129A TRP 3.2 0.2 - - - -
130A ALA* 3.3 20.3 - - - +
131A THR 4.6 0.3 + - - -
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Residues in contact with GLY 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLU* 5.1 2.7 - - - -
83A LEU* 4.9 0.6 - - - +
124A ARG 3.3 8.2 + - - -
125A TYR 3.9 0.2 + - - -
126A MET 3.2 1.0 - - - -
127A ALA* 1.3 76.2 - - - +
129A TRP* 1.3 58.3 + - - +
130A ALA 3.3 0.7 - - - -
131A THR* 4.3 2.9 - - - -
132A LYS* 2.8 41.4 + - - +
124C ARG 6.0 0.4 - - - -
128C GLY* 4.2 10.8 - - - +
132C LYS* 4.2 16.5 - - - -
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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