Contacts of the strand formed by residues 108 - 122 (chain C) in PDB entry 2IZW
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 TYR 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C THR* 5.1 4.3 + - - -
61C ASP 4.9 0.4 - - - -
63C THR* 3.5 37.2 + - + +
104C GLN* 3.4 25.8 - - + +
105C GLY* 3.0 7.0 + - - +
107C ARG* 1.3 89.9 - - + +
109C SER* 1.3 60.1 + - - +
110C LYS 4.1 3.8 - - - +
184C SER* 3.0 22.3 + - - -
225C LEU* 3.3 30.1 - - + -
226C THR 3.5 29.4 - - - +
227C ASP 3.5 2.0 - - - -
228C PRO* 3.8 28.8 - - + +
229C VAL* 3.5 4.3 - - - -
234C ASN* 3.1 6.6 + - - -
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Residues in contact with SER 109 (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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136B MET 5.1 1.6 + - - -
137B LEU* 5.2 1.7 - - - +
138B TYR* 3.8 39.6 + - - +
139B ASP* 6.1 1.8 - - - +
142B ASP* 5.5 3.4 + - - -
108C TYR* 1.3 73.7 - - - +
110C LYS* 1.3 60.9 + - - +
183C LEU* 3.7 4.2 - - - +
184C SER* 2.7 32.1 + - - +
227C ASP* 2.7 23.0 + - - +
228C PRO 4.1 1.2 + - - -
229C VAL* 3.5 20.1 - - - +
234C ASN* 4.4 5.5 + - - -
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Residues in contact with LYS 110 (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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138B TYR* 3.4 35.1 - - + -
172B TYR* 5.2 2.2 + - - -
173B ASP 4.9 1.8 + - - -
176B HIS* 2.7 37.1 + - - +
177B ALA* 3.9 7.5 - - - +
178B SER* 3.3 23.3 + - - +
182B TYR* 5.3 0.2 + - - -
198B PRO 5.1 1.4 + - - -
108C TYR* 4.1 4.7 - - - +
109C SER* 1.3 79.4 - - - +
111C TYR* 1.3 68.9 + - - +
181C TRP* 4.1 8.7 - - + -
182C TYR 3.2 7.2 - - - +
183C LEU* 3.4 20.0 - - + -
184C SER* 4.4 1.2 - - - +
225C LEU* 3.6 1.6 - - - -
226C THR* 3.0 38.6 + - + +
227C ASP* 3.0 24.4 + - - +
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Residues in contact with TYR 111 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90C PHE* 3.5 9.7 + + - -
91C ASN* 3.9 3.4 + - - -
92C VAL* 3.4 40.4 - - + -
110C LYS* 1.3 80.1 - - - +
112C ARG* 1.3 83.0 + - - +
113C VAL* 4.3 13.2 - - + -
181C TRP* 3.5 9.4 - - - -
182C TYR* 2.7 51.9 + - + +
183C LEU 3.5 23.3 - - - -
184C SER* 4.2 0.7 - - - -
196C GLN 2.5 21.9 + - - -
198C PRO* 3.0 25.3 - - + +
223C VAL* 4.8 4.7 - - + -
224C GLU 3.1 16.2 - - - +
225C LEU* 3.6 15.5 - - + -
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Residues in contact with ARG 112 (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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62C ILE* 5.2 3.0 - - - +
111C TYR* 1.3 86.9 - - - +
113C VAL* 1.3 64.8 + - - +
114C ARG* 2.8 38.6 + - - +
180C PRO* 3.6 25.1 + - - +
181C TRP* 3.4 36.9 - - + +
182C TYR* 4.9 8.3 - - + +
223C VAL* 3.4 2.6 - - - +
224C GLU* 2.8 52.5 + - + +
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Residues in contact with VAL 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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90C PHE* 3.9 31.2 - - + -
111C TYR* 4.3 7.2 - - + -
112C ARG* 1.3 76.2 - - - +
114C ARG* 1.3 71.3 + - - +
115C TYR 3.6 23.1 - - - +
116C ALA* 4.0 9.2 - - + -
172C TYR* 3.5 30.5 + - + -
174C PRO* 3.6 19.8 - - - +
182C TYR* 5.8 0.6 - - - -
198C PRO* 4.0 20.9 - - + +
199C PHE* 4.4 1.3 - - + -
222C LEU 3.9 5.6 - - - +
223C VAL* 4.3 4.9 - - + +
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Residues in contact with ARG 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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112C ARG* 2.8 48.7 + - - +
113C VAL* 1.3 81.7 + - - +
115C TYR* 1.3 67.7 + - + +
174C PRO* 3.7 21.9 - - - +
222C LEU* 2.9 39.0 + - + -
224C GLU* 2.9 29.7 + - + +
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Residues in contact with TYR 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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66C LYS* 3.4 33.2 - - + +
113C VAL* 3.5 5.3 - - - +
114C ARG* 1.3 86.0 - - + +
116C ALA* 1.3 65.1 + - - +
117C HIS* 3.3 39.7 - + + +
172C TYR* 5.0 7.2 - - - +
174C PRO* 5.7 0.2 - - - -
220C GLU* 3.8 14.8 - - + +
221C TYR* 3.3 18.0 - - - +
222C LEU* 2.8 62.1 + - + +
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Residues in contact with ALA 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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90C PHE* 4.4 2.5 - - + -
113C VAL* 4.0 13.5 - - + -
115C TYR* 1.3 78.1 - - - +
117C HIS* 1.3 62.7 + - - +
118C PHE* 3.8 26.6 - - + -
170C LEU 3.7 0.7 - - - +
171C SER* 3.3 3.1 - - - -
172C TYR* 2.9 32.8 + - + +
199C PHE* 4.0 10.3 - - + -
220C GLU 3.5 7.9 - - - -
221C TYR* 3.8 10.3 - - + -
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Residues in contact with HIS 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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115C TYR* 3.3 42.7 - + + +
116C ALA* 1.3 79.0 - - - +
118C PHE* 1.3 65.7 + - - +
119C THR* 4.8 4.0 - - + +
169C ARG* 3.2 51.8 + - + +
170C LEU 3.1 4.5 - - - +
171C SER* 2.9 33.7 + - - -
218C MET 3.9 0.3 - - - +
219C ALA* 3.4 4.2 - - - -
220C GLU* 2.8 39.9 + - + +
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Residues in contact with PHE 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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71C LEU* 4.0 23.6 - - + -
90C PHE* 3.8 20.0 - + - -
116C ALA* 3.8 20.2 - - + -
117C HIS* 1.3 74.3 - - - +
119C THR* 1.3 63.4 + - - +
134C MET* 4.5 5.3 - - - +
136C MET* 5.2 3.6 - - - -
166C THR* 4.9 0.3 - - - +
169C ARG* 3.7 4.1 - - - +
170C LEU* 2.7 60.2 + - + +
172C TYR 5.2 0.2 - - - -
199C PHE* 3.7 28.3 - + - -
201C ILE* 3.4 29.4 - - + -
217C ILE* 4.2 9.4 - - + -
218C MET 3.2 6.1 - - - +
219C ALA* 3.4 29.4 - - + -
220C GLU 5.7 0.2 - - - -
221C TYR* 5.6 0.2 - + - -
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Residues in contact with THR 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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117C HIS 4.8 3.4 - - - +
118C PHE* 1.3 79.7 - - - +
120C TRP* 1.3 62.8 + - - +
121C GLU* 3.5 16.2 + - - +
134C MET* 4.4 6.1 - - - -
166C THR* 3.4 19.7 + - - +
169C ARG* 4.9 7.0 - - - -
217C ILE* 3.2 6.7 - - - +
218C MET* 2.7 58.2 + - + +
219C ALA* 5.3 0.4 - - - -
220C GLU 6.0 0.2 - - - +
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Residues in contact with TRP 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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74C VAL* 3.9 24.9 - - + -
119C THR* 1.3 75.6 + - - +
121C GLU* 1.3 81.1 + - - +
122C PRO* 3.5 6.1 - - + +
132C VAL* 3.7 35.1 - - + +
134C MET* 4.4 9.8 - - + +
162C ILE* 2.9 42.7 + - + -
164C SER 3.4 22.0 - - - -
165C PRO* 3.5 2.8 - - - +
166C THR* 3.1 35.9 + - - +
214C LEU* 3.7 11.9 - - + -
215C GLY* 3.2 47.1 - - - -
216C ARG 3.4 18.2 - - - -
217C ILE* 4.0 8.3 - - + -
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Residues in contact with GLU 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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45C GLY 4.3 1.7 - - - -
46C THR* 2.8 43.2 + - - +
48C ILE* 4.8 4.7 - - + -
119C THR* 3.5 13.1 + - - +
120C TRP* 1.3 89.3 - - - +
122C PRO* 1.3 69.8 - - - +
123C ILE* 4.4 1.7 - - - +
165C PRO* 4.1 8.8 - - - +
166C THR 5.1 0.2 + - - -
215C GLY* 3.1 5.5 - - - -
216C ARG* 2.9 39.8 + - + +
218C MET* 3.6 37.2 - - + -
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Residues in contact with PRO 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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44C MET 4.1 15.5 - - - +
45C GLY* 4.4 8.8 - - - -
46C THR 5.2 0.7 + - - -
120C TRP* 3.5 6.3 - - - +
121C GLU* 1.3 89.2 - - + +
123C ILE* 1.3 59.8 + - - +
124C VAL* 3.4 5.8 - - + +
162C ILE 3.5 12.8 - - - +
163C TRP* 3.4 22.9 - - - +
164C SER 3.3 27.8 - - - -
165C PRO* 3.4 26.5 - - + -
214C LEU 3.9 5.2 - - - +
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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