Contacts of the helix formed by residues 274 - 287 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C THR* 4.1 23.1 - - - +
271C ALA* 3.4 28.8 + - - -
273C VAL* 1.3 84.9 - - - +
275C ARG* 1.3 59.0 + - - +
277C GLY* 4.0 3.3 + - - -
278C VAL* 3.7 14.9 + - - +
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Residues in contact with ARG 275 (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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84C THR* 5.6 4.3 - - - -
87C THR* 3.7 24.0 - - + +
261C LYS* 3.6 21.6 + - - +
262C ILE* 3.6 24.6 - - + +
263C CYS 4.1 9.8 + - - +
265C LYS* 3.7 38.4 - - - +
271C ALA 4.1 13.6 + - - +
272C ASP* 2.8 31.8 + - - +
274C SER* 1.3 75.6 - - - +
276C GLU* 1.3 53.1 + - - +
277C GLY 2.5 16.3 + - - -
278C VAL* 2.8 26.4 + - - +
279C GLN 3.7 1.2 + - - -
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Residues in contact with GLU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262C ILE 4.2 0.6 + - - -
263C CYS 4.8 0.8 + - - -
264C LYS* 2.9 41.5 - - + +
272C ASP* 2.8 26.1 + - - +
273C VAL* 3.9 15.4 - - - +
275C ARG* 1.3 69.7 - - - +
277C GLY* 1.3 58.3 + - - +
279C GLN* 3.8 16.1 - - - +
280C ARG* 3.8 38.3 + - - +
320C ILE* 4.1 14.4 - - + +
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Residues in contact with GLY 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C VAL 3.3 15.4 + - - -
274C SER 4.2 2.7 - - - -
275C ARG 2.5 8.7 + - - -
276C GLU* 1.3 74.8 - - - +
278C VAL* 1.3 65.3 + - - -
279C GLN 3.0 1.8 - - - -
280C ARG* 2.8 22.0 + - - +
281C ASP* 2.8 20.9 + - - +
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Residues in contact with VAL 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ALA 3.7 20.0 - - - +
86C PHE* 3.8 37.7 - - + +
87C THR* 4.2 8.5 - - - +
96C VAL* 5.0 1.1 - - + -
262C ILE* 3.7 23.8 - - + -
274C SER 3.7 14.5 + - - +
275C ARG* 2.8 19.7 + - - +
277C GLY* 1.3 69.4 - - - -
279C GLN* 1.3 50.6 + - - +
281C ASP* 2.8 17.1 + - + +
282C LEU* 2.8 39.5 + - + +
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Residues in contact with GLN 279 (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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262C ILE* 2.6 41.8 + - + +
263C CYS* 3.7 2.2 - - - +
264C LYS* 2.4 34.1 + - - +
275C ARG 4.2 2.9 - - - +
276C GLU* 3.8 10.5 - - - +
277C GLY 3.0 0.4 - - - -
278C VAL* 1.3 75.5 - - - +
280C ARG* 1.3 56.1 + - - +
282C LEU* 2.5 31.2 + - - +
283C LEU* 3.0 10.9 + - - +
319C LEU* 3.3 16.3 - - - +
320C ILE* 2.9 47.0 + - + +
323C LEU* 3.9 12.8 - - + +
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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
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82B GLU* 3.2 33.7 - - + +
84B THR* 4.5 21.6 - - - +
258B GLU* 3.5 14.8 + - - -
261B LYS* 3.3 38.7 - - - +
276C GLU* 3.8 37.0 + - - +
277C GLY* 2.8 13.0 + - - +
279C GLN* 1.3 76.9 - - - +
281C ASP* 1.3 60.7 + - - +
283C LEU* 3.6 14.4 - - - +
284C PRO* 3.4 17.5 - - - +
320C ILE* 4.1 25.5 - - + +
322C GLU* 5.6 3.0 + - - -
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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
----------------------------------------------------------
85B LYS* 5.5 10.2 - - - +
86C PHE* 6.2 0.7 - - + -
96C VAL* 3.5 31.5 - - + +
277C GLY* 2.8 27.1 + - - +
278C VAL* 2.8 16.5 + - + +
279C GLN 2.7 4.6 + - - -
280C ARG* 1.3 77.3 - - - +
282C LEU* 1.3 58.7 + - - -
283C LEU 3.4 0.2 - - - -
284C PRO* 3.5 12.2 - - - +
285C LEU* 4.7 0.3 - - - +
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Residues in contact with LEU 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C ALA* 5.4 2.5 - - + -
86C PHE* 5.3 2.7 - - + -
96C VAL* 3.7 24.2 - - + -
99C ILE* 4.0 18.2 - - + -
256C ILE* 3.7 31.0 - - + -
259C ILE* 4.1 19.1 - - + -
262C ILE* 4.3 17.0 - - + -
278C VAL* 2.8 13.9 + - + +
279C GLN* 2.5 16.6 + - - +
281C ASP* 1.3 73.0 - - - +
283C LEU* 1.3 65.9 + - - +
284C PRO* 3.4 0.7 - - - -
285C LEU* 2.9 26.1 + - + +
286C VAL* 3.1 18.7 + - + +
323C LEU* 5.3 8.3 - - + -
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Residues in contact with LEU 283 (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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82B GLU* 4.4 14.4 - - - +
279C GLN 3.0 7.2 + - - +
280C ARG* 3.6 13.7 - - - +
282C LEU* 1.3 76.9 - - - +
284C PRO* 1.3 66.9 - - + +
285C LEU 2.8 1.2 + - - -
286C VAL* 4.5 4.5 - - + -
287C GLU* 2.5 59.4 + - + +
320C ILE* 3.3 29.2 - - + -
322C GLU* 3.5 22.2 - - + +
323C LEU* 4.0 33.9 - - + +
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Residues in contact with PRO 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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82B GLU* 5.5 11.9 - - + +
97C ASP* 5.8 1.3 - - - +
280C ARG 3.4 12.6 - - - +
281C ASP* 3.5 9.2 - - - +
282C LEU 3.5 3.4 - - - -
283C LEU* 1.3 96.3 - - + +
285C LEU* 1.3 60.3 + - + +
287C GLU* 4.4 5.4 - - + +
288C GLY 3.0 18.9 + - - +
289C SER* 2.6 36.4 + - - +
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Residues in contact with LEU 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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96C VAL* 3.9 34.5 - - + +
97C ASP* 3.9 21.8 - - - +
99C ILE* 4.1 20.2 - - + -
100C ILE* 3.8 30.3 - - + -
281C ASP 4.7 0.7 - - - +
282C LEU* 2.9 18.4 + - + +
283C LEU 2.8 3.6 + - - -
284C PRO* 1.3 79.3 - - + +
286C VAL* 1.3 70.0 + - + +
288C GLY* 3.0 9.0 + - - -
289C SER* 4.5 2.7 - - - +
291C VAL* 4.6 1.6 - - + -
300C THR* 3.0 25.5 + - + +
305C PHE* 3.8 18.4 - - + -
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Residues in contact with VAL 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ASN* 4.6 2.9 - - - +
256C ILE* 5.2 5.8 - - + -
282C LEU* 3.1 12.7 + - + +
283C LEU* 3.0 7.4 + - + +
285C LEU* 1.3 82.4 - - - +
287C GLU* 1.3 60.0 + - - +
288C GLY* 3.0 4.0 + - - -
300C THR 4.6 3.1 - - - +
301C ASP 4.9 2.8 - - - +
305C PHE* 3.8 39.7 - - + -
323C LEU* 4.1 23.6 - - + -
326C ARG* 3.2 57.2 + - + +
327C LEU* 5.1 5.2 - - + -
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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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68B ARG* 5.0 7.3 + - - -
80B LYS* 3.3 27.4 + - - +
394B ARG* 4.8 5.1 + - - +
451B ATP 5.1 5.4 + - - -
283C LEU* 2.5 46.0 + - + +
284C PRO* 4.4 4.4 - - + +
286C VAL* 1.3 73.6 - - - +
288C GLY* 1.3 61.7 + - - +
301C ASP* 5.1 1.8 - - - +
322C GLU* 4.3 16.3 - - - +
326C ARG* 3.7 34.6 + - + +
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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