Contacts of the helix formed by residues 295 - 306 (chain L) in PDB entry 3GOK
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 295 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160L GLU* 3.4 13.9 + - - -
293L GLU 3.4 5.1 + - - -
294L VAL* 1.3 77.7 - - - +
296L GLU* 1.3 65.2 - - - +
297L GLU* 4.0 12.9 + - - +
298L VAL* 3.2 35.0 + - - +
299L LYS* 3.4 10.9 + - - +
324L TRP* 5.1 0.2 - - - -
332L PRO* 5.1 6.6 - - - +
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Residues in contact with GLU 296 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294L VAL 3.6 1.2 + - - -
295L SER* 1.3 73.7 - - - +
297L GLU* 1.3 56.9 + - - +
299L LYS* 3.5 20.0 + - - +
300L MET* 3.0 60.4 + - + +
303L ARG* 3.1 18.7 + - - -
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Residues in contact with GLU 297 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295L SER* 3.1 11.5 + - - +
296L GLU* 1.3 79.8 - - - +
298L VAL* 1.3 59.8 + - - +
300L MET* 3.5 6.6 + - - +
301L LEU* 3.2 20.4 + - - +
322L HIS* 4.0 21.0 + - + +
323L PRO* 3.6 26.0 - - - +
324L TRP* 3.9 23.2 - - - +
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Residues in contact with VAL 298 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160L GLU* 3.7 7.6 - - - +
253L MET* 4.5 5.8 - - - -
257L LEU* 3.5 32.1 - - + -
294L VAL* 3.9 7.0 - - + -
295L SER* 3.2 26.4 + - - +
297L GLU* 1.3 72.8 - - + +
299L LYS* 1.3 59.7 + - - +
300L MET 3.1 1.8 - - - -
301L LEU* 3.0 9.1 + - + +
302L ILE* 2.9 30.9 + - + +
324L TRP* 3.3 48.5 - - + +
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Residues in contact with LYS 299 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286L PHE* 3.6 47.1 + - + +
288L ASN* 5.7 0.6 + - - -
291L TRP* 3.2 40.6 + - + +
292L SER* 5.0 2.4 - - - +
294L VAL* 3.2 24.9 + - + +
295L SER 3.4 7.3 + - - +
296L GLU* 3.5 24.1 + - - +
298L VAL* 1.3 78.3 - - - +
300L MET* 1.3 56.4 + - - +
302L ILE* 3.4 2.5 + - - +
303L ARG* 2.9 44.6 + - - +
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Residues in contact with MET 300 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296L GLU* 3.0 49.4 + - + +
297L GLU* 3.6 7.9 - - - +
298L VAL 3.1 0.2 - - - -
299L LYS* 1.3 73.5 - - - +
301L LEU* 1.3 65.5 + - - +
303L ARG* 3.5 26.4 + - - +
304L ASN* 3.2 23.0 + - - +
322L HIS* 6.2 0.2 - - - +
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Residues in contact with LEU 301 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253L MET* 4.0 21.5 - - + -
297L GLU 3.2 10.5 + - - +
298L VAL* 3.0 10.2 + - - +
300L MET* 1.3 76.0 - - - +
302L ILE* 1.3 65.3 + - - +
304L ASN* 3.1 15.2 + - - +
305L LEU* 3.2 17.8 + - + +
314L MET* 3.5 34.1 - - + -
319L PHE* 4.2 14.6 - - + -
322L HIS* 3.6 38.3 + - + +
324L TRP* 4.0 28.5 - - + -
325L ILE* 4.6 2.2 - - + -
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Residues in contact with ILE 302 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250L GLY 4.4 6.3 - - - +
253L MET* 3.6 22.9 - - + -
254L TYR* 4.1 14.4 - - + -
257L LEU* 3.8 20.2 - - + -
284L TYR* 5.0 0.2 - - + -
286L PHE* 4.1 17.0 - - + -
291L TRP* 3.6 33.2 - - + -
298L VAL* 2.9 20.7 + - + +
299L LYS 3.8 6.1 - - - +
301L LEU* 1.3 72.0 - - - +
303L ARG* 1.3 63.3 + - - +
305L LEU* 3.2 9.5 + - - +
306L LEU* 3.0 47.2 + - + +
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Residues in contact with ARG 303 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284L TYR* 3.2 26.6 + - + +
286L PHE* 3.2 28.8 - - + -
296L GLU* 3.1 29.5 + - - -
299L LYS* 2.9 30.4 + - - +
300L MET* 3.7 25.2 - - - +
301L LEU 3.2 0.2 - - - -
302L ILE* 1.3 77.9 - - - +
304L ASN* 1.3 61.3 + - - +
306L LEU 3.5 7.1 + - - -
307L LYS* 3.4 20.2 + - - +
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Residues in contact with ASN 304 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312J GLN* 6.1 0.6 - - - +
300L MET 3.2 12.8 + - - +
301L LEU* 3.1 11.5 + - - +
303L ARG* 1.3 78.1 - - - +
305L LEU* 1.3 60.8 + - - +
307L LYS* 3.7 25.1 - - - +
312L GLN 4.0 7.6 + - - +
313L ARG* 3.6 8.1 - - - +
314L MET* 3.3 51.9 + - + +
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Residues in contact with LEU 305 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246L MET* 3.6 47.6 - - + +
247L TRP* 3.7 11.3 - - - -
249L LEU* 4.2 2.0 - - + -
250L GLY* 3.7 30.1 - - - +
253L MET* 4.0 13.0 - - + -
301L LEU* 3.2 19.7 + - + +
302L ILE* 3.2 4.7 + - - +
304L ASN* 1.3 76.2 - - - +
306L LEU* 1.3 58.3 + - - +
307L LYS 3.3 2.7 - - - -
313L ARG* 3.2 25.9 + - - -
314L MET* 4.1 21.5 - - + -
319L PHE* 3.9 24.0 - - + -
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Residues in contact with LEU 306 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247L TRP* 3.3 37.3 - - + +
250L GLY* 4.0 6.5 - - - +
251L VAL* 3.8 35.4 - - + +
254L TYR* 4.8 0.2 - - + -
262L PRO* 4.2 22.4 - - + -
263L PHE* 4.7 1.6 - - + -
282L GLY* 5.4 1.0 - - - -
284L TYR* 3.9 37.7 + - + +
302L ILE* 3.0 38.1 + - + +
303L ARG 3.5 3.8 + - - -
304L ASN 3.4 0.2 - - - -
305L LEU* 1.3 77.3 - - - +
307L LYS* 1.3 63.8 + - - +
308L THR* 3.3 5.5 + - - +
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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