Contacts of the helix formed by residues 275 - 288 (chain A) in PDB entry 1G3I
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 ARG 275 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A THR* 5.7 4.3 - - + -
87A THR* 3.8 23.1 - - + +
261A LYS 3.6 21.0 + - - +
262A ILE* 3.6 18.3 - - + +
263A CYS 4.0 13.4 + - - +
265A LYS* 3.7 38.7 - - - +
271A ALA 4.2 7.6 + - - +
272A ASP* 3.0 39.0 + - - +
274A SER* 1.3 75.6 - - - +
276A GLU* 1.3 55.2 + - - +
277A GLY 2.4 16.8 + - - -
278A VAL* 2.6 26.3 + - - +
279A GLN 3.7 1.2 + - - -
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Residues in contact with GLU 276 (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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262A ILE 4.0 0.8 + - - -
263A CYS 4.3 0.6 + - - -
264A LYS* 3.2 39.4 - - + +
272A ASP* 2.9 22.7 + - - +
273A VAL* 3.9 15.2 - - - +
275A ARG* 1.3 72.1 - - - +
277A GLY* 1.3 55.8 + - - +
279A GLN* 3.7 22.0 - - - +
280A ARG* 3.8 37.9 + - - +
320A ILE* 4.1 10.9 - - + +
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Residues in contact with GLY 277 (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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273A VAL 3.3 13.6 + - - -
274A SER 4.1 3.1 - - - -
275A ARG 2.4 17.4 + - - -
276A GLU* 1.3 70.9 - - - +
278A VAL* 1.3 57.6 + - - -
279A GLN 2.8 6.2 + - - -
280A ARG* 3.0 11.4 + - - +
281A ASP* 2.6 33.8 + - - +
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Residues in contact with VAL 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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83A ALA 3.7 18.4 - - - +
86A PHE* 3.6 45.3 - - + +
87A THR* 4.2 4.0 - - - +
96A VAL* 4.9 0.7 - - + -
262A ILE* 3.7 23.1 - - + -
274A SER 3.7 12.5 + - - +
275A ARG* 2.6 21.8 + - - +
277A GLY* 1.3 72.1 - - - -
279A GLN* 1.3 57.6 + - - +
281A ASP* 3.1 11.8 + - + +
282A LEU* 2.9 34.6 + - + +
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Residues in contact with GLN 279 (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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262A ILE* 3.1 31.8 + - + +
263A CYS* 4.0 0.6 - - - +
264A LYS* 2.3 40.1 + - - +
275A ARG 4.4 1.3 - - - +
276A GLU* 3.7 14.1 - - - +
277A GLY 2.8 1.0 - - - -
278A VAL* 1.3 73.7 - - - +
280A ARG* 1.3 59.8 + - - +
281A ASP 2.9 0.9 - - - -
282A LEU* 2.7 27.2 + - - +
283A LEU* 3.1 12.3 + - - +
319A LEU* 3.3 18.1 - - + +
320A ILE* 2.8 45.6 + - + +
323A LEU* 3.8 14.6 - - + +
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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
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276A GLU* 3.8 39.8 + - - +
277A GLY* 3.0 8.7 + - - +
279A GLN* 1.3 79.3 - - - +
281A ASP* 1.3 61.4 + - - +
283A LEU* 3.6 14.2 + - - +
284A PRO* 3.4 17.8 - - - +
320A ILE* 4.2 21.6 - - + +
322A GLU* 5.5 3.6 + - - -
82F GLU* 2.8 42.8 - - + +
84F THR* 4.5 17.4 + - - +
258F GLU* 3.4 16.9 + - - -
261F LYS* 4.0 26.6 - - - +
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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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86A PHE* 6.3 0.4 - - + -
96A VAL* 3.3 33.4 - - + +
277A GLY* 2.6 27.7 + - - +
278A VAL* 3.3 15.4 - - + +
279A GLN 2.9 0.2 - - - -
280A ARG* 1.3 80.6 - - - +
282A LEU* 1.3 58.7 + - - +
284A PRO* 3.7 10.1 - - - +
285A LEU* 4.7 1.4 - - - +
85F LYS* 5.0 15.5 - - - +
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Residues in contact with LEU 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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83A ALA* 5.4 2.0 - - + -
86A PHE* 5.1 2.2 - - + -
96A VAL* 3.4 28.0 - - + -
99A ILE* 3.9 18.8 - - + -
256A ILE* 3.6 32.1 - - + -
259A ILE* 4.4 10.3 - - + -
262A ILE* 4.3 20.9 - - + -
278A VAL* 2.9 18.7 + - + +
279A GLN* 2.7 16.2 + - - +
281A ASP* 1.3 73.6 - - - +
283A LEU* 1.3 65.2 + - - +
284A PRO 3.4 0.2 - - - -
285A LEU* 3.0 22.3 + - + +
286A VAL* 3.1 17.5 + - + +
323A LEU* 5.2 7.9 - - + -
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Residues in contact with LEU 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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279A GLN 3.1 7.7 + - - +
280A ARG* 3.6 13.5 - - - +
282A LEU* 1.3 74.2 - - - +
284A PRO* 1.3 66.7 - - + +
285A LEU 2.7 1.7 + - - -
286A VAL* 2.9 6.9 + - + -
287A GLU* 2.5 61.9 + - + +
320A ILE* 3.3 26.2 - - + -
322A GLU* 3.5 31.4 - - + +
323A LEU* 3.9 25.8 - - + +
82F GLU* 4.4 14.4 - - - +
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Residues in contact with PRO 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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97A ASP* 6.0 0.4 - - - +
280A ARG 3.4 12.1 - - - +
281A ASP 3.7 7.6 - - - +
282A LEU 3.5 3.1 - - - -
283A LEU* 1.3 96.1 - - + +
285A LEU* 1.3 59.4 + - + +
287A GLU* 4.3 6.7 - - + +
288A GLY 2.9 21.8 + - - +
289A SER* 2.6 32.9 + - - +
82F GLU* 5.6 6.3 - - + +
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Residues in contact with LEU 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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96A VAL* 3.8 35.9 - - + +
97A ASP* 3.9 21.3 - - - +
99A ILE* 4.0 26.7 - - + -
100A ILE* 3.8 25.1 - - + -
281A ASP 4.7 0.2 - - - +
282A LEU* 3.0 16.5 + - + +
283A LEU 2.7 4.2 + - - -
284A PRO* 1.3 79.2 - - + +
286A VAL* 1.3 67.4 + - + +
288A GLY 3.1 2.8 + - - -
289A SER* 4.6 1.1 - - - +
291A VAL* 4.6 3.4 - - + -
300A THR* 3.0 34.3 + - + +
305A PHE* 3.8 17.4 - - + -
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Residues in contact with VAL 286 (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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52A ASN* 4.4 8.0 + - - +
256A ILE* 5.1 9.6 - - + -
282A LEU* 3.1 10.7 + - + +
283A LEU* 2.9 6.7 + - + +
285A LEU* 1.3 84.4 - - + +
287A GLU* 1.3 61.3 + - + +
288A GLY* 3.3 0.9 + - - -
300A THR 4.5 2.9 - - - +
301A ASP 5.1 2.4 - - - +
305A PHE* 3.8 40.4 - - + -
323A LEU* 4.1 24.0 - - + -
326A ARG* 3.3 50.9 + - + +
327A LEU* 5.4 4.0 - - + -
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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 LEU* 2.5 47.7 + - + +
284A PRO* 4.3 4.3 - - + +
286A VAL* 1.3 72.9 - - - +
288A GLY* 1.3 59.7 + - - +
301A ASP* 5.2 1.4 - - - +
322A GLU* 4.2 14.7 - - - +
326A ARG* 3.8 35.0 + - + +
68F ARG* 4.5 12.5 + - - +
80F LYS* 3.2 28.3 + - - +
394F ARG* 4.9 5.7 + - - +
455F ATP 5.3 1.7 + - - -
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Residues in contact with GLY 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 PRO* 2.9 8.6 + - - +
285A LEU 3.1 5.3 + - - -
286A VAL 3.2 0.4 - - - -
287A GLU* 1.3 81.6 - - - +
289A SER* 1.3 64.7 + - - -
300A THR* 3.2 9.2 - - - -
301A ASP* 3.7 28.7 - - - +
68F ARG* 4.5 17.8 + - - -
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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