Contacts of the strand formed by residues 123 - 134 (chain C) in PDB entry 3IXK
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 123 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116C TYR* 3.5 34.3 - - + +
117C VAL 3.4 12.1 - - - +
118C PRO* 4.1 5.4 - - + -
119C TYR* 4.7 1.6 - - - +
121C GLN 6.0 0.2 - - - +
122C GLY* 1.3 78.9 - - - +
124C TRP* 1.3 64.8 + - - +
153C SER* 3.4 1.4 - - - -
154C ASP* 2.9 66.9 + - + +
156C PHE* 4.0 4.8 - - - +
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Residues in contact with TRP 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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85C ASN* 4.3 11.0 - - + -
87C ALA* 3.3 19.7 - - + -
115C VAL* 3.5 27.8 - - + -
116C TYR* 3.6 8.0 - - - -
117C VAL* 2.9 61.0 + - + +
119C TYR* 2.9 34.0 + + - -
123C LYS* 1.3 76.2 - - - +
125C GLU* 1.3 71.9 - - - +
126C GLY* 4.3 0.7 - - - -
148C ALA* 3.6 24.9 - - + -
150C ILE* 3.8 17.5 - - + -
152C GLU 3.4 14.1 - - - +
153C SER* 3.9 10.1 - - - +
156C PHE* 3.7 30.8 - + + -
166C ILE* 4.2 1.8 - - + +
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Residues in contact with GLU 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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115C VAL 3.3 13.5 - - - +
116C TYR* 4.4 15.0 - - + -
124C TRP* 1.3 81.4 - - - +
126C GLY* 1.3 60.8 + - - +
150C ILE* 3.6 4.9 - - - -
151C THR* 3.0 31.7 + - - +
152C GLU* 3.0 38.6 + - + +
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Residues in contact with GLY 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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114C GLY* 3.2 5.5 - - - -
115C VAL* 2.9 41.6 + - - +
124C TRP* 4.8 1.1 - - - -
125C GLU* 1.3 77.0 - - - +
127C GLU* 1.3 63.5 + - - -
149C ALA 3.2 14.6 - - - -
150C ILE* 4.3 0.4 - - - -
151C THR* 3.3 11.0 - - - -
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Residues in contact with GLU 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C ARG* 2.9 32.5 + - - +
108C TYR* 5.3 0.3 + - - -
110C ASP* 5.2 8.5 - - - +
113C LYS 3.7 7.6 - - - +
114C GLY* 4.5 2.9 - - - -
126C GLY* 1.3 76.1 - - - -
128C LEU* 1.3 66.1 + - - +
147C ILE 4.0 0.2 - - - +
148C ALA* 4.5 1.1 - - - -
149C ALA* 2.8 34.5 + - - +
151C THR* 2.9 27.2 - - + +
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Residues in contact with LEU 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108C TYR* 4.0 5.0 + - - -
110C ASP* 3.4 9.4 - - - +
111C LEU* 3.1 29.6 + - + -
112C ARG 4.2 0.7 + - - -
113C LYS* 2.9 43.0 + - + +
114C GLY 4.2 6.1 - - - +
115C VAL* 3.9 26.5 - - + -
127C GLU* 1.3 76.2 - - - +
129C GLY* 1.3 58.4 + - - +
146C ASN* 5.7 0.4 - - + -
147C ILE 3.7 8.1 - - - +
148C ALA* 4.1 13.0 - - + -
177C PRO* 4.3 14.8 - - + -
181C LEU* 3.9 39.9 - - + -
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Residues in contact with GLY 129 (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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108C TYR* 4.4 9.2 - - - -
109C ARG 3.1 14.8 - - - -
111C LEU* 3.8 12.5 - - - +
128C LEU* 1.3 77.9 - - - +
130C THR* 1.3 60.2 + - - +
146C ASN* 3.5 5.4 - - - +
147C ILE* 2.7 39.4 + - - -
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Residues in contact with THR 130 (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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108C TYR* 3.8 1.7 - - - -
109C ARG* 3.0 42.3 + - + +
111C LEU* 3.9 15.8 - - + +
129C GLY* 1.3 74.3 - - - -
131C ASP* 1.3 64.2 + - - +
144C ARG* 2.8 31.2 + - + -
145C ALA 3.2 11.9 - - - +
146C ASN* 3.4 25.4 - - - +
147C ILE* 4.8 0.9 - - - -
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Residues in contact with ASP 131 (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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69C GLY* 3.2 15.3 + - - -
100C TYR* 2.6 29.4 + - - +
105C SER* 3.0 15.6 + - - -
107C THR* 2.7 31.5 + - - -
108C TYR 3.7 10.6 + - - -
130C THR* 1.3 78.5 - - - +
132C LEU* 1.3 73.6 + - - +
133C VAL* 3.7 5.0 - - - +
143C VAL 3.5 0.2 - - - +
144C ARG* 3.4 8.7 - - - +
145C ALA 3.0 27.9 + - - +
147C ILE* 3.7 13.2 - - + +
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Residues in contact with LEU 132 (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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67C THR 3.7 0.5 - - - +
68C VAL* 3.3 5.9 - - - +
69C GLY 2.9 30.4 + - - +
70C SER* 4.1 7.2 - - - +
107C THR* 3.7 34.8 - - + +
131C ASP* 1.3 82.9 + - - +
133C VAL* 1.3 61.7 + - - +
142C THR* 3.9 20.4 - - + -
143C VAL 3.2 12.3 - - - +
144C ARG* 4.0 28.5 - - + +
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Residues in contact with VAL 133 (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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66C MET* 3.5 32.1 - - + -
67C THR 3.1 10.3 - - - +
68C VAL* 3.9 8.3 - - + -
86C PHE* 3.7 25.6 - - + -
131C ASP 3.7 11.2 - - - +
132C LEU* 1.3 82.0 - - - +
134C SER* 1.3 63.8 + - - +
142C THR* 3.3 5.1 - - - -
143C VAL* 2.8 35.0 + - - +
145C ALA* 4.0 9.4 - - + -
147C ILE* 4.0 6.7 - - + -
184C PHE* 3.6 19.5 - - + -
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Residues in contact with SER 134 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66C MET* 3.5 8.0 - - - +
67C THR* 2.8 46.2 + - - +
133C VAL* 1.3 73.1 + - - +
135C ILE* 1.3 67.0 + - - +
136C PRO* 4.0 2.5 - - - -
139C PRO 6.0 0.2 - - - -
141C VAL* 3.2 10.7 + - - -
142C THR* 2.5 32.2 + - - +
184C PHE* 6.1 0.7 - - - -
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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