Contacts of the helix formed by residues 112 - 124 (chain A) in PDB entry 4L8E
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 GLY 112 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108A TRP* 2.9 14.4 + - - -
110A VAL 3.6 0.6 - - - -
111A ALA* 1.3 80.7 - - - +
113A PHE* 1.3 63.8 + - - +
114A GLY 3.4 0.9 - - - -
115A PRO* 3.6 1.3 - - - -
116A MET* 3.0 36.0 + - - +
141A GLU* 5.8 0.4 - - - -
144A ARG* 6.2 0.4 - - - -
145A LEU* 4.2 12.3 - - - -
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Residues in contact with PHE 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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108A TRP* 3.3 34.0 + + + -
109A GLN* 3.2 24.9 + - + +
112A GLY* 1.3 73.1 - - - +
114A GLY* 1.3 63.6 + - - +
117A LEU* 3.0 59.1 + - + +
145A LEU* 3.9 23.5 - - + +
146A TYR* 3.8 30.7 - + - -
149A LEU* 4.1 17.7 - - + -
171A VAL* 3.7 19.3 - - + -
174A TRP* 3.6 28.3 - - + -
175A ALA* 3.7 9.9 - - + -
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Residues in contact with GLY 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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109A GLN* 2.9 27.8 + - - +
113A PHE* 1.3 75.1 - - - +
115A PRO* 1.3 70.7 - - - +
118A GLY* 2.9 22.7 + - - -
174A TRP* 3.7 19.5 - - - -
301A GSH 3.6 12.6 - - - -
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Residues in contact with PRO 115 (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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109A GLN 3.6 3.8 - - - +
110A VAL* 3.0 28.9 - - - +
111A ALA* 3.6 15.9 - - - +
112A GLY 3.6 9.0 - - - +
114A GLY* 1.3 91.6 - - - +
116A MET* 1.3 74.6 + - + +
118A GLY* 3.8 0.2 - - - -
119A GLN* 3.0 32.0 + - - +
301A GSH 3.4 19.5 - - - +
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Residues in contact with MET 116 (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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111A ALA 5.5 2.0 - - - +
112A GLY* 3.0 24.7 + - - +
115A PRO* 1.3 91.8 - - + +
117A LEU* 1.3 66.3 + - - +
119A GLN* 3.0 16.7 + - + +
120A ASN* 3.0 20.1 + - - +
137A ARG* 5.7 5.4 - - - -
138A TYR* 3.9 28.7 - - + +
141A GLU* 3.7 29.6 - - + +
142A SER* 4.6 2.3 + - - +
145A LEU* 3.6 14.4 - - + -
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Residues in contact with LEU 117 (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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113A PHE* 3.0 63.9 + - + +
116A MET* 1.3 77.6 - - - +
118A GLY* 1.3 57.1 + - - +
120A ASN* 3.2 6.1 + - - +
121A HIS* 2.8 33.4 + - - -
142A SER* 3.2 37.5 - - - +
145A LEU* 4.9 3.1 - - + -
146A TYR* 4.0 8.1 - - + +
174A TRP* 3.7 19.3 - - + -
181A GLN* 3.7 36.6 - - + +
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Residues in contact with GLY 118 (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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114A GLY 2.9 16.5 + - - -
115A PRO 3.8 1.3 - - - -
117A LEU* 1.3 78.2 - - - +
119A GLN* 1.3 60.3 + - - +
121A HIS* 3.4 7.2 + - - +
122A HIS* 3.0 25.1 + - - +
174A TRP* 3.6 9.8 - - - -
301A GSH 3.2 29.1 + - - +
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Residues in contact with GLN 119 (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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115A PRO* 3.0 27.4 + - - +
116A MET* 3.0 16.2 + - + +
118A GLY* 1.3 78.3 + - - +
120A ASN* 1.3 61.7 + - - +
122A HIS* 3.1 9.1 + - - +
123A PHE* 2.9 45.3 + - + -
138A TYR* 3.7 39.4 - - + +
301A GSH 4.7 13.8 + - - +
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Residues in contact with ASN 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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116A MET 3.0 8.6 + - - +
117A LEU* 3.2 10.8 - - - +
119A GLN* 1.3 76.8 - - - +
121A HIS* 1.3 64.7 + - - +
123A PHE* 3.3 3.0 + - - +
124A ASN* 2.8 43.1 + - - -
138A TYR* 3.9 17.7 + - + +
139A THR* 4.4 10.0 + - - +
142A SER* 2.9 33.1 + - - +
181A GLN* 3.2 35.7 + - - +
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Residues in contact with HIS 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 LEU 2.8 25.8 + - - -
118A GLY* 3.5 9.4 - - - +
119A GLN 3.2 0.2 - - - -
120A ASN* 1.3 72.5 - - - +
122A HIS* 1.3 65.9 + - - +
124A ASN* 3.3 14.6 + - - +
125A ARG* 3.7 10.7 - - - +
174A TRP* 3.5 24.5 - + - -
177A CYS* 4.1 12.7 - - + +
180A HIS* 3.7 30.6 + + + +
181A GLN* 3.2 38.1 + - + +
301A GSH 5.3 3.4 - - - +
303A GSH 2.9 42.8 + - + +
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Residues in contact with HIS 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 GLY 3.0 14.0 + - - +
119A GLN* 3.1 15.5 + - - +
121A HIS* 1.3 77.2 - - - +
123A PHE* 1.3 76.6 + + - +
125A ARG* 3.0 44.0 + - - +
126A TYR* 2.7 40.5 + + - -
301A GSH 4.1 26.1 + - - +
305A MES 3.2 33.4 + - - -
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Residues in contact with PHE 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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119A GLN* 2.9 36.1 + - + +
120A ASN* 4.4 2.5 - - - +
122A HIS* 1.3 86.1 - + - +
124A ASN* 1.3 62.0 + - - +
125A ARG 3.0 6.6 + - - -
126A TYR* 3.2 48.1 + + - +
128A PRO* 5.9 0.3 - - - +
131A VAL* 4.0 25.7 - - + +
134A ALA* 3.5 27.1 - - + -
135A ILE* 4.8 17.9 - - - +
138A TYR* 3.7 31.6 - + + -
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Residues in contact with ASN 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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120A ASN* 2.8 38.9 + - - +
121A HIS* 3.6 8.8 - - - +
122A HIS 3.1 1.0 - - - -
123A PHE* 1.3 75.6 - - - +
125A ARG* 1.3 59.4 + - - +
126A TYR 3.2 10.0 + - - +
135A ILE* 4.2 16.3 - - - +
180A HIS* 3.2 28.0 + - + +
182A LYS* 3.4 38.7 + - - +
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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