Contacts of the helix formed by residues 277 - 289 (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 CYS 277 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A SER* 3.8 29.2 - - - -
120C LYS* 4.2 27.1 - - - +
275C CYS* 4.2 5.1 - - - +
276C ALA* 1.3 83.9 - - - +
278C PRO* 1.3 67.2 - - - +
279C GLY 3.3 2.0 - - - -
280C ARG* 3.2 38.3 + - + +
281C ASP* 2.9 25.9 + - - +
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Residues in contact with PRO 278 (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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120C LYS 4.2 1.3 - - - +
122C VAL* 3.4 29.4 - - + +
123C THR 3.9 2.2 - - - +
125C THR* 4.4 4.0 - - - +
134C PHE* 3.4 34.2 - - + +
135C CYS* 3.5 32.3 - - - +
136C GLN* 3.6 8.1 - - + +
275C CYS* 4.1 5.8 - - - +
276C ALA 3.3 13.2 - - - +
277C CYS* 1.3 82.7 - - - +
279C GLY* 1.3 54.3 + - - +
281C ASP* 3.6 0.3 - - - -
282C ARG* 2.8 35.9 + - - +
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Residues in contact with GLY 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C THR* 3.1 33.9 - - - +
119C ALA 3.5 8.3 + - - -
122C VAL* 3.5 12.1 - - - +
125C THR* 4.6 4.0 - - - -
277C CYS 3.3 0.6 - - - -
278C PRO* 1.3 82.8 - - - +
280C ARG* 1.3 63.3 + - - +
282C ARG* 3.2 1.7 + - - +
283C ARG* 3.2 23.4 + - - +
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Residues in contact with ARG 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A SER* 4.7 18.6 - - - +
118C THR 3.8 2.2 + - - -
119C ALA 4.3 2.8 + - - -
120C LYS* 4.6 23.1 - - + +
276C ALA* 6.2 0.8 - - - +
277C CYS* 3.2 36.2 + - + +
279C GLY* 1.3 75.0 - - - +
281C ASP* 1.3 71.1 + - - +
283C ARG* 3.6 22.0 + - - +
284C THR* 3.1 29.4 + - - +
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Residues in contact with ASP 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134C PHE* 4.0 9.4 - - + -
273C ARG* 2.6 43.7 + - - +
275C CYS* 3.4 12.2 - - - +
277C CYS* 2.9 21.2 + - - +
278C PRO 3.8 2.0 - - - +
280C ARG* 1.3 88.7 + - - +
282C ARG* 1.3 68.2 + - - +
284C THR* 4.4 6.1 - - - -
285C GLU* 2.9 31.0 + - + +
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Residues in contact with ARG 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116C SER 3.8 10.1 + - - +
118C THR* 3.8 21.3 - - - +
125C THR* 3.1 36.0 + - + -
126C TYR 3.0 25.0 + - - +
127C SER* 3.7 14.8 - - - -
128C PRO* 3.9 12.9 - - - +
134C PHE* 3.7 21.4 - - + -
278C PRO 2.8 21.3 + - - +
279C GLY 3.7 4.0 - - - +
281C ASP* 1.3 73.3 - - - +
283C ARG* 1.3 59.8 + - - +
285C GLU* 3.3 1.6 + - - +
286C GLU* 2.6 62.9 + - - +
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Residues in contact with ARG 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C THR* 3.0 54.9 + - + -
119C ALA* 4.5 6.7 - - - +
120C LYS* 4.7 3.4 - - - +
279C GLY 3.2 7.8 + - - +
280C ARG* 3.8 24.1 + - - +
282C ARG* 1.3 82.3 - - + +
284C THR* 1.3 57.1 + - - +
286C GLU* 3.2 8.3 + - - +
287C GLU* 2.8 33.9 + - - +
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Residues in contact with THR 284 (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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280C ARG* 3.1 22.2 + - - +
281C ASP* 3.8 7.4 - - - -
282C ARG 3.3 0.2 - - - -
283C ARG* 1.3 76.3 - - - +
285C GLU* 1.3 65.1 + - + +
286C GLU 3.1 0.2 + - - -
287C GLU* 3.1 13.3 - - - +
288C ASN* 2.7 42.9 + - - +
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Residues in contact with GLU 285 (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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130C LEU* 3.7 24.2 - - + +
132C LYS* 2.8 33.6 + - - +
134C PHE* 3.6 7.2 - - + -
271C GLU* 4.7 0.2 - - - +
273C ARG* 3.1 24.8 + - - -
281C ASP* 2.9 25.0 + - + +
282C ARG 3.8 1.6 - - - +
284C THR* 1.3 80.2 - - + +
286C GLU* 1.3 57.3 + - - +
288C ASN* 3.4 9.8 - - - +
289C LEU* 3.2 24.1 + - - +
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Residues in contact with GLU 286 (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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127C SER* 2.6 26.9 + - - +
129C ALA* 4.5 10.7 - - + +
130C LEU* 3.6 17.0 - - + -
282C ARG* 2.6 57.5 + - - +
283C ARG* 3.6 8.4 - - - +
285C GLU* 1.3 74.1 - - - +
287C GLU* 1.3 66.3 + - - +
288C ASN 3.0 1.3 - - - -
289C LEU* 3.2 11.1 + - - +
290C ARG 3.3 10.2 + - - -
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Residues in contact with GLU 287 (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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283C ARG 2.8 20.0 + - - +
284C THR* 3.1 19.2 - - - +
286C GLU* 1.3 73.4 - - - +
288C ASN* 1.3 85.9 + - - +
290C ARG 3.8 5.4 + - - -
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Residues in contact with ASN 288 (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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284C THR* 2.7 27.1 + - - +
285C GLU* 3.4 14.8 - - - +
287C GLU* 1.3 104.8 - - - +
289C LEU* 1.3 66.1 + - - +
1858D ARG* 5.8 5.5 - - - +
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Residues in contact with LEU 289 (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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129C ALA* 4.6 17.9 - - + +
130C LEU* 3.8 27.8 - - + -
285C GLU 3.2 10.8 + - - +
286C GLU 3.2 7.8 + - - +
287C GLU 4.2 0.2 - - - -
288C ASN* 1.3 84.2 - - - +
290C ARG 1.3 50.0 + - - +
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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