Contacts of the helix formed by residues 107 - 126 (chain A) in PDB entry 2R5G
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 LYS 107 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A PRO* 5.7 0.2 - - - -
105A LYS 4.1 2.2 + - - -
106A TYR* 1.3 71.0 - - - +
108A GLU* 1.3 65.2 + - - +
110A PHE* 2.9 32.9 + - + +
111A ASP* 3.2 34.5 + - - +
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Residues in contact with GLU 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A TYR* 3.7 15.1 - - + +
107A LYS* 1.3 85.0 + - - +
109A SER* 1.3 61.3 + - - +
111A ASP* 4.0 14.1 - - + +
112A VAL* 3.1 27.9 + - - +
149A TYR* 3.7 25.5 - - + +
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Residues in contact with SER 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A PRO* 4.3 1.3 - - - -
106A TYR* 3.0 12.2 + - - +
108A GLU* 1.3 77.4 - - - +
110A PHE* 1.3 56.4 + - - +
112A VAL* 3.6 8.1 - - - +
113A GLY* 4.5 1.4 + - - -
149A TYR* 2.7 29.4 + - - -
174A LEU* 3.6 37.1 + - - +
175A ASP* 2.8 24.3 + - - -
182A ALA* 3.6 22.2 - - - +
186A LEU* 5.6 0.2 - - - +
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Residues in contact with PHE 110 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ARG* 3.8 21.8 - - - -
87A GLU* 4.3 5.6 - - - -
104A PRO* 3.3 39.9 - - + -
107A LYS* 2.9 22.0 + - + +
109A SER* 1.3 77.8 - - - +
111A ASP* 1.3 70.3 + - - +
112A VAL 3.3 0.2 - - - -
113A GLY* 3.0 14.2 + - - -
114A CYS* 3.4 18.5 + - - -
181A LEU* 3.8 20.2 - - + -
182A ALA* 3.8 21.1 - - - +
185A SER* 4.5 9.6 + - - -
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Residues in contact with ASP 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LYS* 3.6 43.4 + - - +
108A GLU* 3.2 17.7 + - + +
110A PHE* 1.3 79.4 - - - +
112A VAL* 1.3 63.5 + - - +
113A GLY 3.3 0.5 + - - -
114A CYS* 3.5 6.9 + - - +
115A ASN* 3.3 33.8 + - - +
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Residues in contact with VAL 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLU 3.1 17.8 + - - +
109A SER 3.6 13.0 - - - +
111A ASP* 1.3 76.1 - - - +
113A GLY* 1.3 63.0 + - - +
115A ASN* 4.1 4.1 + - - +
116A LEU* 3.6 21.3 + - - +
142A GLU* 4.9 5.9 - - - +
145A ARG* 4.3 10.3 - - + +
146A LEU* 3.6 53.8 - - + +
149A TYR* 4.2 17.0 - - + -
174A LEU* 4.1 10.8 - - + -
186A LEU* 4.8 0.4 - - + -
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Residues in contact with GLY 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A SER 5.2 0.7 - - - -
110A PHE 3.0 8.9 + - - -
112A VAL* 1.3 82.9 - - - +
114A CYS* 1.3 63.5 + - - +
116A LEU* 3.5 3.4 + - - +
117A PHE* 3.3 22.9 + - - +
185A SER* 6.0 0.9 - - - -
186A LEU* 3.4 38.1 - - - +
189A LYS* 4.4 5.6 - - - +
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Residues in contact with CYS 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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35A ARG* 6.2 0.7 - - - -
110A PHE* 3.4 17.9 + - - +
111A ASP* 3.5 8.2 + - - +
113A GLY* 1.3 73.4 - - - +
115A ASN* 1.3 66.6 + - - +
117A PHE* 3.5 4.2 + - - +
118A ALA* 3.2 22.7 + - - +
185A SER* 4.9 4.0 - - - -
189A LYS* 3.7 24.0 - - - +
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Residues in contact with ASN 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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111A ASP* 3.3 25.7 + - - +
112A VAL* 4.4 2.1 - - - +
113A GLY 3.4 0.4 - - - -
114A CYS* 1.3 74.4 - - - +
116A LEU* 1.3 65.6 + - - +
118A ALA* 3.3 7.7 + - - +
119A LYS* 3.1 33.4 + - - +
142A GLU* 3.3 25.6 + - - +
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Residues in contact with LEU 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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112A VAL 3.6 16.1 + - - +
113A GLY 3.5 4.0 + - - +
114A CYS 3.3 0.6 - - - -
115A ASN* 1.3 78.1 - - - +
117A PHE* 1.3 62.6 + - - +
119A LYS* 3.3 3.5 + - - +
120A PHE* 3.1 21.1 + - - +
139A LEU* 3.8 6.5 - - + -
142A GLU* 3.5 18.6 - - + +
143A PHE* 3.6 49.8 - - + +
146A LEU* 3.8 20.0 - - + -
186A LEU* 4.4 7.9 - - + -
190A LEU* 3.5 32.5 - - + -
193A ILE* 3.8 9.9 - - + -
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Residues in contact with PHE 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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31A PRO* 5.2 6.1 - - + -
113A GLY 3.3 14.9 + - - +
114A CYS* 4.1 3.8 - - - +
115A ASN 3.3 0.2 - - - -
116A LEU* 1.3 79.8 - - - +
118A ALA* 1.3 53.4 + - - +
120A PHE* 3.4 18.6 + + - +
121A SER* 2.8 51.5 + - - -
186A LEU* 6.2 0.2 - - + -
189A LYS* 3.6 50.0 - - + +
192A ILE* 3.9 28.5 - - + -
193A ILE* 4.0 7.9 - - + -
239A TYR* 3.8 19.5 - - - -
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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
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114A CYS 3.2 14.1 + - - +
115A ASN* 3.5 12.6 - - - +
117A PHE* 1.3 74.8 - - - +
119A LYS* 1.3 65.3 + - + +
121A SER* 3.2 8.4 + - - -
122A ALA* 3.0 27.9 + - - +
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Residues in contact with LYS 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASN* 3.1 21.9 + - - +
116A LEU 3.8 5.4 - - - +
118A ALA* 1.3 75.8 - - + +
120A PHE* 1.3 66.3 + - - +
122A ALA* 3.5 7.1 + - + +
123A TYR* 3.1 24.3 + - - +
135A PHE* 4.9 2.1 - - - +
138A SER* 3.6 29.3 + - - +
139A LEU* 4.2 17.2 - - + +
141A LYS* 6.3 0.4 - - - +
142A GLU* 3.3 34.2 + - + +
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Residues in contact with PHE 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 LEU 3.1 11.1 + - - +
117A PHE* 3.6 31.0 - + - +
119A LYS* 1.3 77.2 - - - +
121A SER* 1.3 59.8 + - - +
123A TYR* 3.2 16.7 + + - +
124A ILE* 2.8 60.9 + - + +
139A LEU* 4.0 13.0 - - + +
192A ILE* 4.0 5.8 - - + -
193A ILE* 3.6 40.2 - - + -
196A ALA* 3.7 24.5 - - + -
197A ALA* 4.0 7.6 - - + -
239A TYR* 3.4 27.6 - + - -
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Residues in contact with SER 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 PHE* 2.8 43.2 + - - -
118A ALA* 3.2 8.4 + - - -
120A PHE* 1.3 84.2 - - - +
122A ALA* 1.3 62.7 + - - +
124A ILE* 3.5 6.0 - - - +
125A LYS* 3.1 55.1 + - - +
239A TYR* 5.1 1.4 + - - -
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Residues in contact with ALA 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 3.0 12.9 + - - +
119A LYS* 3.7 11.4 - - + +
120A PHE 3.3 0.2 - - - -
121A SER* 1.3 75.1 - - - +
123A TYR* 1.3 58.1 + - - +
125A LYS* 3.8 4.3 - - - +
126A ASN* 3.0 29.6 + - - +
135A PHE* 3.8 24.7 - - + -
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Residues in contact with TYR 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 LYS 3.1 18.2 + - - +
120A PHE* 3.3 11.0 - + - +
122A ALA* 1.3 77.1 - - - +
124A ILE* 1.3 63.8 + - + +
126A ASN* 3.4 11.4 + - - +
132A ASN* 4.9 5.9 + - + -
135A PHE* 3.7 23.9 - - + +
136A GLU* 3.7 42.8 + - + -
139A LEU* 3.6 28.0 - - + -
197A ALA* 4.0 15.0 - - + -
201A ARG* 2.9 63.2 + - + +
203A PHE* 3.1 22.3 - + + +
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Residues in contact with ILE 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 PHE* 2.8 42.1 + - + +
121A SER* 3.5 13.7 - - - +
123A TYR* 1.3 74.4 - - + +
125A LYS* 1.3 64.1 + - + +
126A ASN 3.5 0.2 - - - -
196A ALA* 3.7 26.2 - - + +
197A ALA* 4.2 1.8 - - - -
200A TYR* 4.1 14.4 - - + -
201A ARG* 3.2 31.5 + - + +
239A TYR* 3.5 43.7 - - + -
242A VAL 3.6 0.9 - - - +
243A ALA* 3.4 21.8 - - + -
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Residues in contact with LYS 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A SER* 3.1 40.0 + - - +
122A ALA* 3.8 3.8 - - - +
124A ILE* 1.3 87.7 - - + +
126A ASN* 1.3 62.7 + - - +
127A THR* 3.1 15.4 + - - +
239A TYR* 5.1 7.9 - - - -
242A VAL* 4.0 26.8 - - + +
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Residues in contact with ASN 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 ALA 3.0 17.3 + - - +
123A TYR 3.4 10.8 + - - +
125A LYS* 1.3 73.6 - - - +
127A THR* 1.3 55.5 + - - +
128A GLN* 2.8 43.8 + - - +
131A ALA* 3.8 2.9 - - - +
132A ASN* 2.9 19.6 + - - +
135A PHE* 3.4 38.6 - - + -
201A ARG* 3.1 9.0 + - - -
242A VAL 5.3 0.6 - - - +
244A LYS 4.9 0.5 - - - +
245A GLN* 2.8 28.1 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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