Contacts of the helix formed by residues 277 - 291 (chain A) 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 CYS 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A LYS* 3.3 33.9 - - - -
275A CYS* 3.5 4.6 - - - -
276A ALA* 1.3 80.2 - - + +
278A PRO* 1.3 67.9 - - - +
279A GLY 3.3 2.0 - - - -
280A ARG* 3.2 58.9 + - + +
281A ASP* 2.9 23.4 + - - +
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Residues in contact with PRO 278 (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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122A VAL* 3.6 19.5 - - + +
123A THR 3.6 9.6 - - - +
125A THR* 4.0 7.2 - - + -
134A PHE* 3.5 32.7 - - + +
135A CYS* 3.5 32.5 - - - +
136A GLN* 3.6 6.5 - - + +
275A CYS* 3.7 6.8 - - - +
276A ALA 3.2 13.0 - - - +
277A CYS* 1.3 83.4 - - - +
279A GLY* 1.3 57.8 + - - +
281A ASP 3.6 0.3 - - - -
282A ARG* 2.8 31.9 + - - +
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 3.4 27.3 - - - +
119A ALA 3.6 2.7 + - - -
122A VAL* 3.2 26.8 - - - +
125A THR* 4.3 4.3 - - - -
277A CYS* 3.3 1.2 - - - -
278A PRO* 1.3 81.5 - - - +
280A ARG* 1.3 62.9 + - - +
282A ARG* 3.2 2.3 + - - +
283A ARG* 3.2 19.4 + - - +
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Residues in contact with ARG 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A LYS* 4.6 9.1 - - + +
273A ARG* 5.3 3.0 - - - +
275A CYS* 5.5 0.4 - - - +
276A ALA* 4.6 10.5 - - - +
277A CYS* 3.2 51.9 + - - +
279A GLY* 1.3 75.7 - - - +
281A ASP* 1.3 87.0 + - - +
283A ARG* 3.6 25.7 + - - +
284A THR* 3.0 32.0 + - - +
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Residues in contact with ASP 281 (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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134A PHE* 3.9 10.5 - - + -
273A ARG* 2.7 44.7 + - - +
275A CYS* 3.1 12.9 - - - +
277A CYS 2.9 19.7 + - - +
278A PRO 3.8 2.5 - - - +
280A ARG* 1.3 95.2 + - - +
282A ARG* 1.3 67.0 + - - +
284A THR* 4.2 7.0 + - - +
285A GLU* 2.9 30.9 + - + +
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Residues in contact with ARG 282 (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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115A HIS* 5.6 4.8 + - - -
116A SER 3.3 16.8 + - - -
117A GLY 3.5 4.2 + - - -
118A THR* 3.7 19.4 - - - +
125A THR* 3.0 33.9 + - + -
126A TYR 3.3 23.4 + - - -
127A SER* 3.8 2.8 - - - +
128A PRO* 3.8 14.1 - - - +
134A PHE* 3.6 31.6 - - + -
278A PRO 2.8 21.5 + - - +
279A GLY 3.2 3.8 + - - +
281A ASP* 1.3 72.5 - - - +
283A ARG* 1.3 54.8 + - - +
285A GLU* 3.3 1.6 + - - +
286A GLU* 2.8 69.5 + - - +
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Residues in contact with ARG 283 (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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118A THR* 2.9 58.2 + - + -
119A ALA* 4.7 0.6 - - - +
120A LYS* 3.2 48.2 - - - +
279A GLY 3.2 3.0 + - - +
280A ARG* 3.7 22.8 + - - +
282A ARG* 1.3 80.5 - - - +
284A THR* 1.3 57.1 + - - +
286A GLU* 3.2 9.0 + - - +
287A GLU* 2.9 34.0 + - + +
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Residues in contact with THR 284 (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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280A ARG* 3.0 21.7 + - - +
281A ASP* 3.7 10.1 + - - +
282A ARG 3.3 0.2 - - - -
283A ARG* 1.3 78.7 + - - +
285A GLU* 1.3 56.2 + - + +
287A GLU* 3.0 8.5 + - - +
288A ASN* 2.7 37.2 + - + +
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Residues in contact with GLU 285 (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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130A LEU* 4.0 21.5 - - + +
132A LYS* 2.8 34.4 + - - +
134A PHE* 3.1 21.9 - - + -
273A ARG* 3.9 17.1 + - - -
281A ASP* 2.9 18.3 + - + +
282A ARG 4.0 2.0 - - - +
284A THR* 1.3 80.8 - - + +
286A GLU* 1.3 60.7 + - - +
288A ASN* 3.2 26.2 - - + +
289A LEU* 3.2 9.7 + - - +
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Residues in contact with GLU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A THR* 4.9 4.0 - - - +
127A SER* 2.8 22.9 + - - -
128A PRO* 4.8 0.2 - - - +
129A ALA* 4.2 14.2 + - + +
130A LEU* 3.8 15.9 - - + -
282A ARG* 2.8 63.8 + - + +
283A ARG* 3.6 9.6 - - - +
285A GLU* 1.3 74.5 - - - +
287A GLU* 1.3 63.3 + - - +
289A LEU* 3.2 19.7 - - - +
290A ARG* 3.6 9.4 + - - +
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Residues in contact with GLU 287 (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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283A ARG* 2.9 14.2 + - + +
284A THR* 3.4 9.6 - - - +
286A GLU* 1.3 72.2 - - - +
288A ASN* 1.3 68.2 + - - +
289A LEU 2.8 4.0 + - - -
290A ARG* 2.9 59.4 + - + +
291A LYS 3.9 1.7 + - - +
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Residues in contact with ASN 288 (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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284A THR* 2.7 16.9 + - + +
285A GLU* 3.2 23.3 - - - +
287A GLU* 1.3 77.2 - - - +
289A LEU* 1.3 56.1 + - - +
291A LYS 2.8 24.6 - - - +
292A LYS* 5.2 2.1 - - - +
1858B ARG* 6.0 4.8 - - - +
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Residues in contact with LEU 289 (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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129A ALA* 6.0 5.6 - - + -
130A LEU* 3.5 31.4 - - + -
285A GLU 3.2 6.0 + - - +
286A GLU* 3.2 15.5 - - - +
287A GLU 2.8 0.8 + - - -
288A ASN* 1.3 80.4 - - - +
290A ARG* 1.3 56.1 + - - +
291A LYS* 2.6 19.8 + - - +
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Residues in contact with ARG 290 (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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286A GLU 3.7 10.5 - - - +
287A GLU* 2.9 49.4 + - - +
289A LEU* 1.3 75.5 - - - +
291A LYS* 1.3 62.4 + - + +
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Residues in contact with LYS 291 (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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287A GLU 3.9 1.4 + - - -
288A ASN* 2.8 20.3 + - - +
289A LEU 2.6 7.8 + - - +
290A ARG* 1.3 80.2 - - + +
292A LYS* 1.3 126.1 + - + +
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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