Contacts of the helix formed by residues 286 - 300 (chain C) in PDB entry 4GID
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 LYS 286 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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284C LEU 3.2 3.5 + - - -
285C PRO* 1.3 68.9 - - - +
287C LYS* 1.3 62.8 + - + +
289C PHE* 3.3 5.5 + - + +
290C GLU* 2.8 68.5 + - + +
374C GLN* 2.9 33.0 + - + +
375C SER 3.2 15.7 + - - +
376C SER* 6.0 0.7 - - - -
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Residues in contact with LYS 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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263C MET* 3.6 18.6 - - + +
267C GLU* 3.0 40.0 + - - +
270C TYR* 6.2 2.7 - - + -
285C PRO* 3.0 4.1 + - + +
286C LYS* 1.3 79.8 - - + +
288C VAL* 1.3 63.7 + - + +
290C GLU* 3.6 6.9 + - - +
291C ALA* 3.2 22.3 + - - +
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Residues in contact with VAL 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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254C VAL* 5.2 3.8 - - + -
261C LEU* 4.1 15.4 - - + +
263C MET* 3.8 15.5 - - + -
267C GLU* 3.4 32.8 - - + +
268C TYR* 3.9 25.6 - - + -
284C LEU* 4.3 22.2 - - + -
285C PRO* 2.8 27.2 + - + +
287C LYS* 1.3 70.1 - - + +
289C PHE* 1.3 57.8 + - - +
291C ALA* 3.2 2.3 + - - +
292C ALA* 2.8 36.4 + - - +
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Residues in contact with PHE 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C LEU* 3.8 22.6 - - + +
285C PRO 2.8 10.6 + - - +
286C LYS 3.4 8.7 - - - +
288C VAL* 1.3 77.6 - - - +
290C GLU* 1.3 79.6 + - - +
292C ALA* 3.7 0.7 - - - +
293C VAL* 2.9 58.6 + - + +
310C TRP 4.0 16.6 - - - -
311C LEU* 5.5 5.2 - - + -
370C PHE* 4.5 0.4 - + - -
372C ILE* 3.5 30.7 - - + -
373C SER* 3.5 23.3 - - - -
374C GLN* 3.7 35.9 - - + -
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Residues in contact with GLU 290 (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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286C LYS* 2.8 55.6 + - + +
287C LYS* 3.8 7.4 - - - +
288C VAL 3.2 0.2 - - - -
289C PHE* 1.3 97.1 - - - +
291C ALA* 1.3 62.8 + - - +
293C VAL* 3.5 5.9 + - - +
294C LYS* 3.0 24.3 + - - +
374C GLN* 4.8 0.5 + - - -
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Residues in contact with ALA 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261C LEU* 3.8 16.3 - - + +
263C MET* 3.9 21.1 - - + -
287C LYS 3.2 11.4 + - - +
288C VAL 3.2 7.5 + - - +
290C GLU* 1.3 79.0 - - - +
292C ALA* 1.3 63.5 + - - +
294C LYS* 3.4 8.8 + - - +
295C SER* 3.1 23.4 + - - -
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Residues in contact with ALA 292 (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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254C VAL* 6.1 0.9 - - + -
256C ILE* 4.9 8.1 - - + -
261C LEU* 4.2 18.8 - - + +
284C LEU* 4.0 20.9 - - + -
288C VAL 2.8 20.8 + - - +
289C PHE 3.7 4.0 - - - +
291C ALA* 1.3 73.8 - - - +
293C VAL* 1.3 58.3 + - + +
295C SER* 3.1 4.3 + - - -
296C ILE* 2.8 43.8 + - + +
331C ILE* 6.4 0.2 - - + -
372C ILE* 5.7 1.6 - - + -
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Residues in contact with VAL 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289C PHE* 2.9 54.7 + - + +
290C GLU* 3.9 7.6 - - - +
292C ALA* 1.3 76.9 - - + +
294C LYS* 1.3 58.8 + - - +
296C ILE* 3.9 7.2 - - + +
297C LYS* 2.7 59.3 + - + +
310C TRP* 4.3 14.6 - - + +
370C PHE* 4.1 18.6 - - + -
372C ILE* 5.7 1.3 - - + -
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Residues in contact with LYS 294 (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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290C GLU 3.0 17.4 + - - +
291C ALA* 3.7 8.5 - - - +
292C ALA 3.2 0.2 - - - -
293C VAL* 1.3 78.0 - - - +
295C SER* 1.3 58.5 + - - +
297C LYS* 3.6 8.6 - - - +
298C ALA* 2.9 29.2 + - + +
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Residues in contact with SER 295 (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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256C ILE* 3.4 31.6 + - - +
259C GLN* 4.7 14.3 + - - +
261C LEU* 4.3 7.4 - - - +
291C ALA 3.1 13.4 + - - -
292C ALA 3.1 7.9 + - - -
294C LYS* 1.3 76.8 - - - +
296C ILE* 1.3 61.3 + - - +
298C ALA* 3.3 6.4 + - - +
299C ALA* 2.9 28.9 + - - +
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Residues in contact with ILE 296 (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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256C ILE* 4.2 11.7 - - + -
292C ALA* 2.8 36.4 + - + +
293C VAL* 3.9 4.7 - - + +
295C SER* 1.3 72.1 - - - +
297C LYS* 1.3 62.1 + - - +
299C ALA* 3.3 2.4 + - - +
300C SER* 3.0 26.6 + - - +
310C TRP* 3.6 25.1 - - + -
328C PHE* 4.8 3.6 - - + -
329C PRO* 4.1 30.9 - - + +
331C ILE* 3.9 24.9 - - + -
353C TYR* 4.3 7.4 - - + +
370C PHE* 4.1 24.0 - - + -
372C ILE* 4.2 5.2 - - + -
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Residues in contact with LYS 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C VAL* 2.7 34.4 + - + +
294C LYS* 3.6 8.1 - - - +
296C ILE* 1.3 77.0 - - - +
298C ALA* 1.3 62.3 + - - +
300C SER* 3.2 7.9 + - - -
301C SER* 3.0 24.1 + - - -
304C LYS* 5.4 0.9 + - - -
307C ASP* 5.2 7.5 + - - +
310C TRP* 3.4 54.6 - - + +
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Residues in contact with ALA 298 (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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298A ALA* 4.6 15.4 - - - +
301A SER* 4.8 14.1 - - - +
294C LYS* 2.9 19.1 + - + +
295C SER* 3.6 7.4 - - - +
297C LYS* 1.3 75.9 - - - +
299C ALA* 1.3 62.1 + - - +
301C SER* 3.1 22.9 + - - -
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Residues in contact with ALA 299 (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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259A GLN* 3.3 14.4 + - - +
298A ALA 5.9 0.7 - - - -
299A ALA* 6.2 4.0 - - - +
256C ILE* 5.0 1.8 - - + -
257C ASN* 4.7 9.2 - - + +
295C SER* 2.9 17.4 + - - +
296C ILE 3.8 4.5 - - - +
297C LYS 3.3 0.2 - - - -
298C ALA* 1.3 76.3 - - - +
300C SER* 1.3 58.3 + - - +
301C SER* 3.5 0.9 + - - -
302C THR* 5.3 0.7 + - - +
327C ILE 3.2 11.3 - - - +
329C PRO* 3.8 30.7 - - + -
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Residues in contact with SER 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A GLN* 4.9 0.2 - - - -
296C ILE 3.0 17.4 + - - -
297C LYS* 3.2 4.9 + - - -
299C ALA* 1.3 76.5 - - - +
301C SER* 1.3 61.5 + - - +
302C THR* 3.0 6.6 + - - -
303C GLU* 2.9 21.7 + - - +
305C PHE* 4.2 4.1 - - - -
310C TRP* 3.9 19.4 - - - -
327C ILE* 3.5 28.8 - - - +
328C PHE* 4.1 20.8 - - - -
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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