Contacts of the helix formed by residues 274 - 282 (chain S) 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 SER 274 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272S ASP* 4.0 16.1 - - - +
273S VAL* 1.3 76.7 - - - +
275S ARG* 1.3 62.8 + - - +
276S GLU 3.1 1.6 - - - -
277S GLY* 3.1 17.1 + - - +
278S VAL* 3.2 19.8 + - - +
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Residues in contact with ARG 275 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261S LYS* 3.7 23.6 + - - +
262S ILE* 2.7 45.0 - - + +
263S CYS 4.4 10.1 + - - +
264S LYS* 6.0 0.2 - - - -
265S LYS 4.2 16.0 + - - -
269S SER* 4.0 13.0 + - - +
272S ASP* 3.7 34.2 + - - +
273S VAL 3.0 0.8 - - - -
274S SER* 1.3 81.4 - - - +
276S GLU* 1.3 55.8 + - - +
277S GLY 3.3 0.9 - - - -
278S VAL* 4.2 3.0 + - - +
279S GLN* 3.8 7.1 + - - +
273X VAL* 5.4 13.1 - - - +
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Residues in contact with GLU 276 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262S ILE 4.4 2.7 - - - +
264S LYS* 4.5 28.4 + - + +
273S VAL* 3.1 28.2 + - + +
275S ARG* 1.3 77.5 - - - +
277S GLY* 1.3 61.1 + - - +
278S VAL 3.5 0.4 - - - -
279S GLN* 4.0 10.1 - - - +
280S ARG* 3.2 37.0 + - - +
320S ILE* 3.8 27.3 - - + +
261T LYS* 5.5 4.2 + - - -
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Residues in contact with GLY 277 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273S VAL 3.4 4.6 + - - -
274S SER* 3.1 13.6 + - - -
276S GLU* 1.3 78.3 - - - +
278S VAL* 1.3 53.5 + - - +
280S ARG* 2.8 9.1 + - - +
281S ASP* 2.7 43.7 + - - +
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Residues in contact with VAL 278 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83S ALA* 4.7 12.6 - - + +
96S VAL* 6.0 4.3 - - + -
262S ILE* 4.4 22.0 - - + -
274S SER 3.2 13.8 + - - +
275S ARG* 4.5 5.8 - - - +
277S GLY* 1.3 71.0 - - - +
279S GLN* 1.3 56.7 + - - +
280S ARG 2.8 13.7 + - - -
281S ASP* 3.1 8.6 + - - +
282S LEU* 3.0 42.2 + - + +
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Residues in contact with GLN 279 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262S ILE* 3.0 42.2 - - + +
263S CYS* 4.1 3.1 - - - -
264S LYS 5.2 0.5 + - - -
275S ARG 3.8 10.7 + - - +
276S GLU* 4.0 10.0 - - - +
278S VAL* 1.3 79.5 - - - +
280S ARG* 1.3 58.2 + - - +
282S LEU* 4.2 6.3 - - - +
283S LEU 4.1 2.6 + - - -
318S ASP 4.5 0.3 - - - +
319S LEU* 3.1 30.2 - - + +
320S ILE* 2.4 73.4 - - + +
323S LEU* 3.5 24.6 - - + +
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Residues in contact with ARG 280 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276S GLU* 3.2 26.6 + - - +
277S GLY* 2.8 14.1 + - - +
278S VAL 2.8 2.0 + - - -
279S GLN* 1.3 77.6 - - - +
281S ASP* 1.3 57.7 + - - +
282S LEU 2.9 5.4 - - - -
283S LEU* 2.9 30.9 + - - +
284S PRO* 3.3 4.5 - - - +
320S ILE* 3.5 32.1 - - - +
322S GLU* 3.7 12.7 + - - -
82T GLU* 4.0 36.2 + - + +
258T GLU* 3.2 28.5 + - - +
261T LYS* 3.4 34.1 - - - +
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Residues in contact with ASP 281 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96S VAL* 3.0 41.7 - - + +
277S GLY* 2.7 27.2 + - - +
278S VAL* 3.1 6.5 + - - +
280S ARG* 1.3 73.3 - - - +
282S LEU* 1.3 55.7 + - - +
283S LEU 3.2 1.3 - - - -
284S PRO* 3.4 16.1 - - - +
285S LEU* 4.2 4.7 - - - +
82T GLU* 5.2 8.3 - - - +
83T ALA 5.6 1.6 - - - +
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Residues in contact with LEU 282 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81S VAL* 6.2 0.2 - - + -
83S ALA* 6.2 2.0 - - + -
96S VAL* 3.3 27.1 - - + -
99S ILE* 3.6 25.1 - - + -
256S ILE* 3.5 37.0 - - + -
259S ILE* 6.1 1.6 - - + -
262S ILE* 5.5 7.6 - - + -
278S VAL* 3.0 30.6 + - + +
279S GLN* 4.4 6.5 - - - +
280S ARG 2.9 0.8 - - - -
281S ASP* 1.3 77.6 - - - +
283S LEU* 1.3 61.3 + - - +
284S PRO 3.6 0.4 - - - -
285S LEU* 3.9 12.1 + - + +
286S VAL* 3.6 23.5 + - + +
323S LEU* 4.9 8.8 - - + +
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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