Contacts of the helix formed by residues 295 - 306 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160D GLU* 3.3 15.4 + - - -
293D GLU 3.4 5.8 + - - -
294D VAL* 1.3 76.5 - - - +
296D GLU* 1.3 66.2 + - - +
297D GLU* 3.1 12.3 + - - +
298D VAL* 3.1 36.4 + - - +
299D LYS* 3.4 8.8 + - - +
324D TRP* 5.0 0.2 - - - -
332D PRO* 5.1 6.3 - - - +
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Residues in contact with GLU 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294D VAL 3.7 1.0 + - - -
295D SER* 1.3 73.7 - - - +
297D GLU* 1.3 57.3 + - - +
299D LYS* 3.4 20.7 + - - +
300D MET* 3.0 60.4 + - + +
303D ARG* 3.1 18.2 + - - -
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Residues in contact with GLU 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295D SER* 3.1 11.2 + - - +
296D GLU* 1.3 79.3 - - - +
298D VAL* 1.3 58.8 + - - +
300D MET* 3.5 7.1 + - - +
301D LEU* 3.3 19.8 + - - +
322D HIS* 3.9 21.6 + - + +
323D PRO* 3.5 27.0 - - - +
324D TRP* 3.9 22.3 - - - +
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Residues in contact with VAL 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D GLU* 3.7 6.3 - - - +
253D MET* 4.5 5.6 - - - -
257D LEU* 3.6 30.7 - - + -
294D VAL* 4.0 6.5 - - + -
295D SER* 3.1 27.1 + - - +
297D GLU* 1.3 74.2 - - + +
299D LYS* 1.3 59.4 + - - +
300D MET 3.1 1.8 - - - -
301D LEU* 3.1 8.1 + - + +
302D ILE* 2.9 31.9 + - + +
324D TRP* 3.3 46.9 - - + +
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Residues in contact with LYS 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286D PHE* 3.5 52.3 + - + +
288D ASN* 5.9 0.4 + - - -
291D TRP* 3.4 31.9 + - + +
292D SER* 5.3 1.8 + - - +
294D VAL* 3.3 25.2 + - + +
295D SER 3.4 7.6 + - - +
296D GLU* 3.7 24.5 + - - +
298D VAL* 1.3 77.4 - - - +
300D MET* 1.3 57.5 + - - +
302D ILE* 4.6 2.7 - - - +
303D ARG* 2.9 44.1 + - - +
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Residues in contact with MET 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296D GLU* 3.0 48.3 + - + +
297D GLU* 3.6 8.1 - - - +
299D LYS* 1.3 75.9 - - - +
301D LEU* 1.3 62.9 + - - +
303D ARG* 3.5 24.8 + - - +
304D ASN* 3.1 23.4 + - - +
322D HIS* 6.2 0.2 - - - +
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Residues in contact with LEU 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D MET* 3.9 28.3 - - + -
297D GLU 3.3 10.6 + - - +
298D VAL* 3.1 9.3 + - - +
300D MET* 1.3 76.7 - - - +
302D ILE* 1.3 65.0 + - - +
304D ASN* 3.2 13.7 + - - +
305D LEU* 3.2 17.2 + - + +
314D MET* 3.7 29.8 - - + -
319D PHE* 4.1 17.0 - - + -
322D HIS* 3.9 37.2 + - + +
324D TRP* 4.0 22.2 - - + -
325D ILE* 4.6 2.9 - - + -
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Residues in contact with ILE 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250D GLY 4.4 7.2 - - - +
253D MET* 3.6 24.0 - - + -
254D TYR* 4.2 14.8 - - + -
257D LEU* 3.8 19.1 - - + -
284D TYR* 4.9 0.2 - - + -
286D PHE* 4.1 16.2 - - + -
291D TRP* 3.8 32.3 - - + -
298D VAL* 2.9 20.1 + - + +
299D LYS 3.8 4.0 - - - +
301D LEU* 1.3 76.2 - - - +
303D ARG* 1.3 62.0 + - - +
305D LEU* 3.2 8.4 + - + +
306D LEU* 3.1 44.7 + - + +
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Residues in contact with ARG 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284D TYR* 3.3 26.4 + - + +
286D PHE* 3.2 28.7 - - + -
296D GLU* 3.1 28.7 + - - -
299D LYS* 2.9 30.4 + - - +
300D MET* 3.6 24.2 - - - +
301D LEU 3.3 0.2 - - - -
302D ILE* 1.3 76.9 - - - +
304D ASN* 1.3 60.6 + - - +
306D LEU 3.6 7.3 + - - -
307D LYS* 3.5 21.6 + - - +
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Residues in contact with ASN 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300D MET 3.1 16.3 + - - +
301D LEU* 3.5 7.9 - - - +
302D ILE 3.1 0.4 - - - -
303D ARG* 1.3 76.8 - - - +
305D LEU* 1.3 61.2 + - - +
306D LEU 3.4 0.4 - - - -
307D LYS* 3.9 24.8 - - - +
312D GLN 4.0 7.9 + - - -
313D ARG* 3.7 7.6 - - - +
314D MET* 3.4 50.8 + - + +
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Residues in contact with LEU 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246D MET* 3.6 46.9 - - + +
247D TRP* 3.7 12.0 - - - -
249D LEU* 4.3 1.3 - - + -
250D GLY* 3.7 28.9 - - - +
253D MET* 3.9 25.6 - - + -
301D LEU* 3.2 20.2 + - + +
302D ILE* 3.2 4.9 + - - +
304D ASN* 1.3 75.3 - - - +
306D LEU* 1.3 59.2 + - - +
307D LYS 3.3 2.5 - - - -
313D ARG* 3.2 25.3 + - - -
314D MET* 4.2 15.7 - - + +
319D PHE* 3.9 16.8 - - + -
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Residues in contact with LEU 306 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247D TRP* 3.3 37.7 - - + +
250D GLY* 4.0 6.1 - - - +
251D VAL* 3.8 36.3 - - + +
254D TYR* 4.9 0.7 - - + -
262D PRO* 4.3 20.2 - - + -
263D PHE* 4.6 1.8 - - + -
282D GLY* 5.5 1.0 - - - -
284D TYR* 3.8 38.2 - - + +
302D ILE* 3.1 38.1 + - + +
303D ARG 3.8 3.8 - - - -
304D ASN 3.4 0.2 - - - -
305D LEU* 1.3 77.6 - - - +
307D LYS* 1.3 63.1 + - - +
308D THR* 3.4 5.4 + - - +
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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