Contacts of the strand formed by residues 251 - 258 (chain C) in PDB entry 1GZH
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 ILE 251 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161C ALA* 4.2 10.1 - - + -
162C ILE 3.2 11.4 - - - +
163C TYR* 3.4 35.7 - - + -
164C LYS 4.0 0.9 - - - +
173C VAL* 3.9 11.2 - - + -
194C LEU* 3.7 17.3 - - + -
236C TYR* 4.6 10.3 - - + -
240C SER* 5.5 1.1 - - - +
246C MET* 3.4 30.3 - - + -
249C ARG 4.9 0.2 - - - +
250C PRO* 1.3 72.1 - - - +
252C LEU* 1.3 78.4 + - - +
253C THR* 5.2 0.9 - - - +
271C GLU* 3.5 2.8 - - - +
272C VAL* 3.1 47.2 + - + +
274C VAL* 5.3 1.6 - - + -
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Residues in contact with LEU 252 (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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100C GLN* 3.4 35.4 - - + +
160C MET 3.6 0.5 - - - +
161C ALA* 3.1 5.9 - - - -
162C ILE* 2.8 44.2 + - + +
164C LYS* 3.8 34.3 - - + +
251C ILE* 1.3 88.8 - - - +
253C THR* 1.3 64.6 + - - +
254C ILE* 3.8 4.4 + - + -
269C SER* 4.7 12.3 - - - +
270C PHE 3.5 10.1 - - - +
271C GLU* 3.5 22.0 - - + +
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Residues in contact with THR 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159C ALA* 4.6 5.4 - - + -
160C MET 3.5 4.7 - - - +
161C ALA* 4.4 2.3 - - - +
195C ILE* 4.2 17.6 - - + +
234C TYR* 5.9 1.3 - - + -
236C TYR* 2.7 33.2 + - - +
251C ILE* 5.2 0.5 - - - +
252C LEU* 1.3 73.9 - - - +
254C ILE* 1.3 61.1 + - - +
255C ILE* 3.9 16.5 + - + -
269C SER* 3.1 24.3 - - - -
270C PHE* 2.9 38.2 + - + -
272C VAL* 3.2 11.8 - - - +
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Residues in contact with ILE 254 (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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98C PRO* 4.6 7.0 - - + -
99C SER 3.6 26.5 - - - +
100C GLN* 4.1 9.0 - - + -
158C ARG* 3.6 1.2 - - - +
159C ALA* 3.6 3.5 - - - -
160C MET* 2.6 41.8 + - + +
162C ILE* 3.4 45.8 - - + -
252C LEU* 4.4 5.4 - - + +
253C THR* 1.3 74.3 - - - +
255C ILE* 1.3 61.2 + - - +
256C THR* 3.9 22.6 + - + +
267C ARG* 4.0 11.7 - - + -
268C ASN 3.6 4.7 - - - +
269C SER* 4.0 9.9 - - - -
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Residues in contact with ILE 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109C PHE* 3.8 22.8 - - + -
111C LEU* 4.2 17.7 - - + -
143C VAL* 4.6 2.2 - - + -
145C LEU* 4.1 7.9 - - + -
157C VAL* 3.9 17.9 - - + -
158C ARG 3.3 5.6 - - - +
159C ALA* 3.9 9.6 - - + -
234C TYR* 3.7 30.1 - - + +
253C THR* 3.9 20.4 + - + -
254C ILE* 1.3 71.0 - - - +
256C THR* 1.3 64.4 + - - +
267C ARG* 3.3 2.9 - - - -
268C ASN 2.8 40.8 + - - +
270C PHE* 4.0 21.3 - - + -
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Residues in contact with THR 256 (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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109C PHE* 4.7 1.1 - - - -
156C ARG 3.7 0.5 - - - +
157C VAL* 3.5 5.7 - - - +
158C ARG* 2.9 56.9 + - - +
254C ILE* 3.9 21.7 + - + +
255C ILE* 1.3 79.9 - - - +
257C LEU* 1.3 64.3 + - - +
258C GLU* 3.9 8.9 + - - -
264C LEU* 4.3 12.1 - - + -
266C GLY 3.3 5.8 - - - +
267C ARG* 3.9 19.7 - - + +
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Residues in contact with LEU 257 (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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107C TYR* 4.9 11.2 - - + -
109C PHE* 3.9 43.7 - - + -
145C LEU* 4.7 2.0 - - + -
147C VAL* 4.2 15.0 - - + -
151C PRO* 4.6 14.1 - - + -
155C THR* 4.0 12.3 - - + -
156C ARG 3.5 3.6 - - - +
157C VAL* 3.7 29.2 - - + -
220C TYR* 4.3 11.9 - - + -
256C THR* 1.3 72.6 - - - +
258C GLU* 1.3 53.6 + - - +
264C LEU* 3.8 1.6 - - - +
265C LEU* 2.7 35.5 + - + +
266C GLY* 2.7 23.5 + - - +
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Residues in contact with GLU 258 (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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155C THR* 3.0 5.5 - - - +
156C ARG* 2.7 54.5 + - + +
158C ARG* 2.8 50.8 + - - -
217C VAL* 4.3 5.9 - - - +
256C THR* 3.9 11.2 + - - +
257C LEU* 1.3 74.4 - - - +
259C ASP* 1.3 67.0 + - - +
262C GLY* 3.9 23.3 - - - +
263C ASN 3.1 16.2 - - - +
264C LEU* 4.7 1.6 - - + +
265C LEU* 3.2 6.3 - - - +
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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