Contacts of the strand formed by residues 112 - 127 (chain A) in PDB entry 5IXG
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 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 THR* 3.3 1.5 - - - -
109A LEU 3.0 28.4 + - - +
110A HIS* 3.6 15.5 - - + +
111A GLY* 1.3 80.1 - - - +
113A THR* 1.4 62.4 + - - +
114A LYS* 3.7 31.6 - - + +
148A ASP 3.7 12.3 - - - +
149A PHE* 3.3 28.5 - - - +
150A GLY* 5.3 1.3 - - - -
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Residues in contact with THR 113 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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106A ASN* 3.9 29.2 - - + +
107A LEU 3.2 5.2 - - - +
108A THR* 2.8 29.4 + - - +
111A GLY 4.2 1.6 + - - -
112A VAL* 1.4 71.4 - - - +
114A LYS* 1.3 78.4 + - - +
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Residues in contact with LYS 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 ASN* 3.3 7.2 - - - +
107A LEU* 2.9 32.3 + - - +
112A VAL* 3.7 13.1 + - + +
113A THR* 1.3 83.3 - - - +
115A PRO* 1.3 80.0 - - + +
148A ASP* 2.8 45.3 + - + +
149A PHE* 3.5 26.7 - - + -
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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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105A GLY 3.4 10.1 - - - +
106A ASN* 3.6 9.4 - - - +
114A LYS* 1.3 101.0 - - + +
116A LEU* 1.3 62.8 + - - +
144A PHE* 5.9 1.9 - - - +
149A PHE* 5.3 1.4 - - - -
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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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89A TYR* 2.9 39.5 + - + -
105A GLY 2.9 20.8 + - - +
107A LEU* 4.1 30.5 - - + -
114A LYS 3.5 0.6 + - - -
115A PRO* 1.3 77.5 - - - +
117A THR* 1.4 76.5 + - - +
118A LEU* 4.0 20.4 - - + -
143A GLU 3.7 31.9 - - - +
144A PHE* 4.5 10.8 - - + -
149A PHE* 5.8 2.0 - - + -
165A LEU* 4.0 17.7 - - + -
201A OTP 5.6 2.5 - - + -
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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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102A SER* 4.3 8.1 - - - +
103A VAL 3.2 11.0 - - - +
104A VAL* 3.9 29.4 - - + +
116A LEU* 1.4 81.4 - - - +
118A LEU* 1.3 77.2 + - - +
119A LYS* 4.2 1.5 + - + +
141A VAL 4.2 0.3 - - - +
142A GLY* 4.0 8.5 - - - -
143A GLU 4.8 0.9 + - - +
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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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89A TYR* 3.8 33.7 - - + +
102A SER* 3.1 5.7 - - - -
103A VAL* 2.8 43.3 + - + +
116A LEU* 4.0 19.7 - - + -
117A THR* 1.3 83.5 - - - +
119A LYS* 1.3 59.4 + - - +
120A ILE* 4.6 0.4 - - - +
140A ALA* 4.6 4.5 - - + -
141A VAL 3.4 9.6 - - - +
142A GLY* 4.1 7.9 - - - -
165A LEU* 4.7 2.9 - - + -
167A ILE* 3.7 31.2 - - + -
201A OTP 3.8 34.5 - - + -
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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
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101A VAL 3.8 8.7 - - - +
102A SER* 4.4 3.4 - - - +
117A THR* 4.1 2.9 + - + +
118A LEU* 1.3 71.0 - - - +
120A ILE* 1.3 76.8 + - - +
121A ASP* 2.6 39.4 + - - +
140A ALA* 3.1 3.6 - - - -
141A VAL* 2.8 48.0 + - + +
143D GLU* 4.6 12.8 - - - +
162D LYS* 3.3 41.7 - - + +
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Residues in contact with ILE 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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93A ILE* 4.6 3.8 - - + -
100A PRO* 3.7 35.7 - - + +
101A VAL* 2.9 24.3 + - - +
102A SER* 3.9 16.8 - - - +
103A VAL* 4.0 22.9 - - + -
118A LEU 4.6 0.4 - - - +
119A LYS* 1.3 86.2 + - - +
121A ASP* 1.3 59.0 + - - +
122A SER* 3.3 28.3 - - - +
123A PHE* 4.2 4.0 - - + -
138A VAL* 4.1 17.5 - - + -
139A ASP 3.7 4.3 - - - +
140A ALA* 4.2 10.1 - - + -
201A OTP 4.6 8.3 - - + -
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Residues in contact with ASP 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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119A LYS* 2.6 48.5 + - - +
120A ILE* 1.3 73.0 - - - +
122A SER* 1.3 63.1 + - - +
139A ASP* 2.8 21.7 + - + +
141A VAL* 3.5 30.2 - - - +
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Residues in contact with SER 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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99A LYS* 5.8 1.6 - - - +
120A ILE* 3.3 11.5 - - - +
121A ASP* 1.3 80.2 - - - +
123A PHE* 1.3 63.2 + - - +
138A VAL* 3.2 19.6 - - - -
139A ASP* 3.2 25.9 + - - +
27B GLY 4.5 13.4 + - - -
28B LEU 5.2 1.6 + - - -
29B SER* 5.7 1.4 - - - -
30B VAL* 5.7 1.0 - - - +
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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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44A LEU* 3.8 17.3 - - + -
46A ARG* 3.8 23.8 - - - -
99A LYS* 3.0 51.4 + - + +
100A PRO* 3.8 33.0 - - + -
120A ILE* 4.2 10.1 - - + -
122A SER* 1.3 78.5 - - - +
124A LYS* 1.3 66.1 + - - +
125A CYS* 3.2 35.2 - - - -
136A CYS* 4.1 2.0 - - + -
137A GLY 3.3 8.1 - - - -
138A VAL* 3.8 17.7 - - + -
201A OTP 3.9 22.4 - - + -
27B GLY 5.6 0.2 - - - -
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Residues in contact with LYS 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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123A PHE* 1.3 79.5 - - - +
125A CYS* 1.3 74.0 + - - +
126A MET* 3.5 25.7 - - - +
136A CYS* 3.3 2.1 - - - +
137A GLY 2.8 31.7 + - - -
25B PHE 2.9 25.1 + - - -
26B GLY* 2.9 21.5 + - - +
27B GLY* 3.9 11.4 - - - +
28B LEU* 3.6 22.4 - - + +
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Residues in contact with CYS 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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9A TYR* 5.1 0.4 - - - -
44A LEU* 5.1 0.4 - - - -
46A ARG* 4.0 15.7 - - - +
123A PHE* 3.2 31.5 - - - -
124A LYS* 1.3 80.7 - - - +
126A MET* 1.3 65.0 + - - +
134A GLU* 3.6 18.2 - - - +
135A VAL 3.2 4.5 - - - +
136A CYS* 2.1 43.5 - - - -
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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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124A LYS* 3.5 32.8 - - - +
125A CYS* 1.3 77.5 - - - +
127A PRO* 1.3 84.2 - - + +
129A PRO* 4.7 8.7 - - + -
134A GLU* 3.6 6.4 - - - +
135A VAL* 2.9 42.9 + - + +
25B PHE* 3.8 31.4 - - + +
28B LEU* 4.1 15.0 - - + -
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Residues in contact with PRO 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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126A MET* 1.3 101.8 - - + +
128A HIS* 1.3 66.8 + - - +
129A PRO* 3.4 8.1 - - - +
132A LYS* 5.9 3.4 - - - -
133A ARG 4.0 6.7 - - - +
134A GLU* 4.5 3.6 - - - -
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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