Contacts of the helix formed by residues 113 - 128 (chain A) in PDB entry 4RG7
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 SER 113 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A PRO* 5.8 5.1 - - - +
73A TYR* 5.5 5.6 - - - -
110A PHE* 3.2 20.5 + - - -
112A ASP* 1.3 88.6 + - - +
114A ALA* 1.3 67.1 + - - +
115A CYS 3.1 3.1 - - - -
116A PHE* 2.9 23.4 + - - -
117A THR* 2.9 20.5 - - - +
18B HIS* 3.3 23.2 + - - -
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Residues in contact with ALA 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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106A ILE* 4.8 0.9 - - + -
107A VAL* 3.7 39.5 - - + +
110A PHE* 3.5 12.6 - - + +
111A GLY 3.2 19.1 + - - +
113A SER* 1.3 76.8 - - - +
115A CYS* 1.3 57.5 + - - +
117A THR* 3.4 4.7 + - - -
118A LEU* 3.0 41.0 + - + +
144A LEU* 5.1 6.3 - - + -
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Residues in contact with CYS 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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112A ASP 3.3 21.5 + - - -
113A SER 3.0 0.4 + - - -
114A ALA* 1.3 79.8 - - - +
116A PHE* 1.3 84.2 + - - +
119A SER* 3.0 13.3 + - - -
141A SER* 2.8 36.6 + - - +
144A LEU* 4.3 9.0 - - + +
145A ASN* 3.6 41.7 - - + +
14B GLN* 5.1 2.5 - - - -
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Residues in contact with PHE 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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73A TYR* 3.4 24.7 + - + +
112A ASP 4.1 2.9 - - - -
113A SER* 2.9 13.1 + - - +
115A CYS* 1.3 94.1 - - - +
117A THR* 1.3 55.8 + - - +
119A SER* 3.1 9.0 - - - -
120A LEU* 2.6 32.4 + - - +
145A ASN* 4.9 6.1 - - - -
14B GLN* 3.4 36.3 - - + -
15B ALA* 3.4 27.1 - - + -
18B HIS* 3.2 43.5 - + + -
20B ALA* 4.0 16.2 - - + -
23B ASP* 5.9 1.8 - - - -
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Residues in contact with THR 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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73A TYR* 3.4 25.6 - - + -
92A LEU* 3.8 9.8 - - - +
106A ILE* 3.9 7.3 - - - +
110A PHE* 3.0 45.0 - - + -
113A SER* 2.9 22.9 - - - +
114A ALA 3.4 4.9 + - - -
116A PHE* 1.3 73.0 - - - +
118A LEU* 1.3 57.7 + - - +
120A LEU* 3.4 8.4 - - - +
121A LEU* 2.5 38.9 + - - +
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Residues in contact with LEU 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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103A HIS* 4.7 10.5 - - + -
106A ILE* 4.2 29.6 - - + -
107A VAL* 4.5 13.0 - - + -
114A ALA* 3.0 31.3 + - + +
115A CYS* 4.7 0.4 - - - +
117A THR* 1.3 77.0 + - - +
119A SER* 1.3 57.0 + - - +
121A LEU* 4.2 3.4 - - + -
122A GLY* 2.5 33.8 + - - -
137A CYS* 3.5 43.2 - - - +
140A LYS* 4.2 14.8 - - + +
141A SER* 3.9 22.9 - - - +
144A LEU* 5.4 2.0 - - + -
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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
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115A CYS 3.0 17.5 + - - -
116A PHE* 3.1 15.2 - - - -
118A LEU* 1.3 80.7 - - - +
120A LEU* 1.3 54.6 + - - -
122A GLY* 3.6 0.9 - - - -
123A HIS* 3.0 28.1 + - - +
138A TYR* 3.6 16.9 - - - -
141A SER* 3.1 11.3 + - - -
148A LEU* 5.3 1.2 - - - +
150A SER* 6.4 0.4 - - - -
151A PRO* 3.3 19.9 - - - +
23B ASP* 4.8 5.2 + - - -
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Residues in contact with LEU 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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73A TYR* 4.1 17.7 - - + +
76A ALA* 3.9 17.9 - - + -
77A LYS* 3.8 47.1 - - + +
80A VAL* 3.7 32.3 - - + -
92A LEU* 3.9 9.9 - - + -
116A PHE 2.6 20.3 + - - +
117A THR* 3.1 7.8 + - - +
119A SER* 1.3 73.8 - - - +
121A LEU* 1.3 63.8 + - - +
123A HIS* 3.2 20.3 + - + +
124A VAL* 3.2 16.8 + - + +
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Residues in contact with LEU 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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89A GLU* 4.3 20.6 - - + -
92A LEU* 3.8 22.9 - - + +
93A SER* 4.3 12.1 - - - -
106A ILE* 3.7 29.8 - - + -
117A THR* 2.5 20.7 + - - +
118A LEU* 3.8 6.1 - - + +
120A LEU* 1.3 69.0 - - - +
122A GLY* 1.3 64.4 + - - +
124A VAL* 3.1 23.7 - - + +
125A TYR* 3.0 58.5 + - + +
137A CYS* 4.1 11.2 - - - -
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Residues in contact with GLY 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 LEU 2.5 23.4 + - - -
119A SER 3.6 2.0 - - - -
121A LEU* 1.3 75.1 - - - +
123A HIS* 1.3 61.9 + - - +
125A TYR* 3.3 1.9 + - - +
126A CYS* 3.0 27.6 + - - -
134A GLY* 3.8 10.3 - - - -
137A CYS* 3.7 16.0 - - - +
138A TYR* 3.5 11.0 - - - -
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Residues in contact with HIS 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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80A VAL* 4.2 25.1 - - + +
119A SER 3.0 12.9 + - - +
120A LEU* 3.2 15.2 + - + +
122A GLY* 1.3 73.7 - - - +
124A VAL* 1.3 60.0 + - + +
126A CYS* 3.4 4.2 + - - +
127A LYS* 2.9 38.4 + - + +
138A TYR* 3.1 17.1 + - - +
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Residues in contact with VAL 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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80A VAL* 4.1 30.5 - - + -
85A LEU* 4.0 36.3 - - + +
88A GLY* 5.6 1.6 - - - -
89A GLU* 5.2 8.7 - - + +
92A LEU* 5.9 1.1 - - + -
120A LEU* 3.3 11.9 - - + +
121A LEU* 3.1 36.1 - - + +
123A HIS* 1.3 75.2 - - + +
125A TYR* 1.3 52.5 + - + +
127A LYS* 3.5 5.3 - - + +
128A THR* 2.5 46.3 + - + +
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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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89A GLU* 3.6 27.5 + - + -
93A SER* 3.5 27.0 + - - -
121A LEU* 3.0 44.5 + - + +
124A VAL* 1.3 78.5 - - + +
126A CYS* 1.3 55.5 + - - +
128A THR* 3.4 10.4 + - - -
129A ASP 3.4 0.3 + - - -
130A ARG* 2.7 44.3 + - + +
133A LYS* 3.9 23.6 - - + -
134A GLY* 3.5 18.6 - - - +
137A CYS* 3.6 27.8 - - - -
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Residues in contact with CYS 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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122A GLY 3.0 24.6 + - - +
123A HIS* 3.6 6.5 - - - +
125A TYR* 1.3 78.7 - - - +
127A LYS* 1.3 60.3 + - - +
128A THR 3.1 0.2 - - - -
129A ASP* 3.3 13.0 + - - -
130A ARG 4.2 2.8 + - - +
131A LEU* 4.5 12.6 + - + +
134A GLY* 3.8 14.4 - - - -
135A SER 4.5 0.2 - - - -
138A TYR* 3.6 26.7 - - - +
158A ILE* 4.0 20.2 - - + -
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Residues in contact with LYS 127 (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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123A HIS* 2.9 34.3 + - + +
124A VAL* 3.5 5.6 - - + +
126A CYS* 1.3 76.5 - - - +
128A THR* 1.3 62.5 + - + +
129A ASP 3.5 0.8 + - - -
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Residues in contact with THR 128 (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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85A LEU* 4.1 27.1 - - + +
86A ALA* 5.4 2.5 - - + +
89A GLU* 5.7 0.5 + - - -
124A VAL* 2.5 28.5 + - + +
125A TYR* 3.4 10.9 + - - -
126A CYS 3.1 0.4 - - - -
127A LYS* 1.3 82.1 - - + +
129A ASP* 1.3 68.9 + - - +
130A ARG* 3.4 6.7 + - - +
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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