Contacts of the strand formed by residues 112 - 127 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108C THR* 3.3 1.9 - - - +
109C LEU 2.9 31.7 + - - +
110C HIS* 3.7 10.8 - - - +
111C GLY* 1.3 84.6 - - - +
113C THR* 1.3 65.4 + - - +
114C LYS* 3.7 24.9 - - + -
148C ASP 3.6 21.3 - - - +
149C PHE* 3.4 28.2 - - + +
150C GLY* 5.4 0.9 - - - -
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Residues in contact with THR 113 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ASN* 3.9 27.6 - - + +
107C LEU 3.3 3.8 - - - +
108C THR* 2.6 33.1 + - - +
111C GLY 4.3 0.4 + - - -
112C VAL* 1.3 72.2 - - - +
114C LYS* 1.3 69.9 + - - +
115C PRO* 4.9 0.2 - - - +
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Residues in contact with LYS 114 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106C ASN* 3.5 6.5 - - - -
107C LEU* 2.9 34.3 + - - +
112C VAL* 3.7 14.8 - - + +
113C THR* 1.3 80.5 - - - +
115C PRO* 1.3 76.8 - - + +
148C ASP* 2.7 53.4 + - + +
149C PHE* 3.7 17.6 - - + -
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Residues in contact with PRO 115 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105C GLY 3.4 10.5 - - - +
106C ASN* 3.3 10.7 - - - +
114C LYS* 1.3 94.2 - - + +
116C LEU* 1.4 61.5 + - - +
144C PHE* 5.9 1.6 - - - +
149C PHE* 5.3 2.3 - - - -
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Residues in contact with LEU 116 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C TYR* 2.9 36.0 + - + -
105C GLY 2.9 19.5 + - - +
107C LEU* 4.0 33.2 - - + -
114C LYS 3.5 1.0 + - - -
115C PRO* 1.4 75.2 - - - +
117C THR* 1.4 78.5 + - - +
118C LEU* 4.0 15.0 - - + -
142C GLY* 4.8 0.4 - - - -
143C GLU 3.5 33.7 - - - +
144C PHE* 4.4 9.6 - - + -
149C PHE* 6.0 1.3 - - + -
165C LEU* 4.0 23.3 - - + -
201C OTP 5.8 1.3 - - + -
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Residues in contact with THR 117 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102C SER* 4.4 2.0 - - - -
103C VAL 3.2 9.6 - - - +
104C VAL* 3.9 30.1 - - + +
116C LEU* 1.4 87.2 - - - +
118C LEU* 1.3 69.0 + - - +
119C LYS* 3.8 29.0 + - + +
141C VAL 4.3 0.2 - - - +
142C GLY* 4.0 8.0 - - - -
143C GLU 4.8 0.3 + - - -
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Residues in contact with LEU 118 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C TYR* 3.9 32.1 - - + +
102C SER* 3.1 5.2 - - - -
103C VAL* 2.7 45.5 + - + +
116C LEU* 4.0 20.4 - - + -
117C THR* 1.3 78.9 - - - +
119C LYS* 1.3 60.7 + - - +
140C ALA* 4.4 10.1 - - + -
141C VAL 3.4 4.3 - - - +
142C GLY* 4.1 17.0 - - - +
165C LEU* 4.6 6.3 - - + -
167C ILE* 4.3 17.9 - - + -
201C OTP 3.8 36.6 - - + -
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Residues in contact with LYS 119 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B GLU* 4.1 24.0 - - - +
162B LYS* 5.9 5.6 - - + -
101C VAL* 3.8 11.9 - - + +
102C SER* 3.9 10.0 + - - -
117C THR* 3.8 25.9 - - + +
118C LEU* 1.3 71.3 - - - +
120C ILE* 1.3 63.0 + - - +
121C ASP* 3.4 7.6 + - - +
140C ALA* 3.1 3.8 - - - -
141C VAL* 2.7 52.2 + - + +
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Residues in contact with ILE 120 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LYS* 5.9 0.9 + - - -
93C ILE* 4.6 4.7 - - + -
99C LYS* 6.1 0.2 - - - -
100C PRO* 3.8 32.0 - - + +
101C VAL* 2.9 25.0 + - - +
102C SER* 3.8 28.9 - - - +
103C VAL* 4.0 15.7 - - + -
118C LEU 4.6 0.4 - - - +
119C LYS* 1.3 72.9 - - - +
121C ASP* 1.3 61.1 + - - +
122C SER 3.3 29.2 - - - +
123C PHE* 4.0 8.3 - - + -
138C VAL* 4.6 8.3 - - + -
139C ASP 3.8 4.5 - - - +
140C ALA* 4.3 9.0 - - + -
201C OTP 4.8 10.8 - - + -
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Residues in contact with ASP 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162B LYS* 5.5 4.9 + - - -
119C LYS* 3.4 7.1 + - - +
120C ILE* 1.3 77.5 - - - +
122C SER* 1.3 62.3 + - - +
139C ASP* 2.8 21.7 + - + +
141C VAL* 3.6 38.1 - - - +
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Residues in contact with SER 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C LYS* 5.6 1.3 - - - +
120C ILE* 3.3 11.0 - - - +
121C ASP* 1.3 78.4 - - - +
123C PHE* 1.3 60.6 + - - +
137C GLY 4.4 0.2 - - - -
138C VAL* 3.2 7.0 - - - -
139C ASP* 3.1 44.2 + - - +
27D GLY 4.5 14.0 + - - -
28D LEU 5.3 0.7 + - - -
29D SER* 5.7 1.2 - - - -
30D VAL* 5.6 1.7 - - - +
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Residues in contact with PHE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C LEU* 3.9 15.9 - - + -
46C ARG* 3.9 20.6 - - - -
99C LYS* 3.3 40.7 + - + +
100C PRO* 3.8 40.4 - - + -
120C ILE* 4.0 10.3 - - + -
122C SER* 1.3 77.2 - - - +
124C LYS* 1.3 63.4 + - - +
125C CYS* 3.3 34.1 - - - -
136C CYS* 4.6 1.1 - - + -
137C GLY 3.3 6.1 - - - -
138C VAL* 3.5 17.9 - - + -
201C OTP 3.6 23.1 - - + -
27D GLY 5.4 0.2 - - - -
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Residues in contact with LYS 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123C PHE* 1.3 78.4 - - - +
125C CYS* 1.3 70.2 + - - +
126C MET* 3.8 25.9 - - - +
136C CYS* 3.3 2.6 - - - +
137C GLY 2.7 37.5 + - - +
25D PHE 3.0 16.2 + - - -
26D GLY* 2.8 23.9 + - - +
27D GLY* 3.9 15.3 - - - +
28D LEU* 3.6 26.4 - - + +
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Residues in contact with CYS 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9C TYR* 4.9 0.2 - - - -
44C LEU* 4.5 1.6 - - - -
46C ARG* 3.7 26.0 - - - +
123C PHE* 3.3 30.9 - - - -
124C LYS* 1.3 76.1 - - - +
126C MET* 1.3 64.3 + - - +
134C GLU* 3.8 12.3 - - - +
135C VAL 3.3 4.0 - - - -
136C CYS* 2.1 45.8 - - - -
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Residues in contact with MET 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C LYS* 3.8 34.1 - - - +
125C CYS* 1.3 77.8 - - - +
127C PRO* 1.3 87.8 - - + +
128C HIS* 3.4 0.6 + - - -
129C PRO* 4.1 16.4 - - + -
134C GLU* 3.4 7.8 - - - +
135C VAL* 2.9 46.7 + - + +
25D PHE* 4.1 16.4 - - + +
28D LEU* 4.1 25.1 - - + -
157D TYR 6.0 0.2 - - - +
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Residues in contact with PRO 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126C MET* 1.3 96.6 - - + +
128C HIS* 1.3 65.2 + - - +
129C PRO* 3.4 8.0 - - - +
132C LYS* 6.0 1.8 - - - -
133C ARG 3.8 8.5 - - - +
134C GLU* 4.4 4.9 - - + -
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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