Contacts of the helix formed by residues 306 - 321 (chain B) in PDB entry 6EKK
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 ASP 306 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B LEU* 4.4 15.7 - - + +
164B PRO 3.9 14.1 - - - +
165B SER* 3.7 14.5 + - - +
305B GLY* 1.3 71.6 - - - -
307B GLY* 1.3 59.9 + - - +
308B VAL 3.3 2.7 - - - -
309B ALA* 3.3 4.9 + - - +
310B ARG* 2.8 58.3 + - - +
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Residues in contact with GLY 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296B ARG* 5.6 0.5 - - - +
301B SER* 5.9 0.9 - - - -
302B THR* 4.0 26.1 - - - +
304B THR 4.2 3.4 + - - -
305B GLY 3.2 5.5 + - - -
306B ASP* 1.3 81.6 + - - +
308B VAL* 1.3 56.2 + - - +
310B ARG* 3.3 6.2 + - - +
311B ALA* 2.9 29.5 + - - +
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Residues in contact with VAL 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B ILE* 3.8 16.2 - - + -
172B LEU* 4.0 31.6 - - + -
176B PHE* 3.9 23.1 - - + -
184B MET* 4.4 8.1 - - + -
217B MET* 4.4 0.4 - - - -
297B LEU* 4.1 18.6 - - + -
302B THR* 3.8 27.7 + - - +
305B GLY 4.9 0.8 + - - -
306B ASP 3.3 0.4 - - - -
307B GLY* 1.3 74.3 - - - +
309B ALA* 1.3 63.5 + - - +
311B ALA* 3.2 11.1 + - - +
312B PHE* 3.2 28.7 + - + -
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Residues in contact with ALA 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 3.9 19.7 - - + +
164B PRO* 3.6 41.1 - - + +
172B LEU* 4.2 4.0 - - + +
217B MET* 4.1 15.0 - - + +
306B ASP 3.3 5.8 + - - +
308B VAL* 1.3 79.0 - - - +
310B ARG* 1.3 57.1 + - - +
312B PHE* 3.4 2.4 + - - +
313B LEU* 2.9 29.8 + - - +
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Residues in contact with ARG 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163B LEU* 3.5 18.4 - - + +
306B ASP* 2.8 45.7 + - - +
307B GLY* 3.7 7.9 - - - +
308B VAL 3.3 0.2 - - - -
309B ALA* 1.3 76.3 - - - +
311B ALA* 1.3 57.5 + - - +
313B LEU* 3.3 15.3 + - - +
314B LYS* 2.9 48.7 + - - +
384B VAL* 4.4 20.1 + - - +
387B GLU* 5.6 5.9 + - - +
388B GLU* 3.4 24.2 + - - -
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Residues in contact with ALA 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B LEU* 3.5 26.7 - - + +
296B ARG* 3.8 38.5 + - + +
297B LEU* 4.0 9.0 - - + -
302B THR* 5.9 0.2 - - + -
307B GLY 2.9 14.1 + - - +
308B VAL 3.2 10.3 + - - +
310B ARG* 1.3 76.8 - - - +
312B PHE* 1.3 62.2 + - - +
314B LYS* 3.3 5.5 + - - +
315B ALA* 3.1 16.6 + - - +
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Residues in contact with PHE 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B TYR* 5.6 1.1 - + - -
184B MET* 3.7 38.8 - - + -
185B LEU* 5.0 0.7 - - + -
188B TYR* 3.7 39.7 + + + -
217B MET* 3.4 52.9 - - + +
293B LEU* 3.8 19.3 - - + -
297B LEU* 3.8 30.5 - - + -
308B VAL* 3.2 21.6 + - + -
309B ALA 3.9 1.8 - - - +
311B ALA* 1.3 76.2 - - - +
313B LEU* 1.3 60.4 + - - +
315B ALA* 3.2 3.8 + - - +
316B GLN* 2.8 33.7 + - - +
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Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B LEU* 4.1 16.4 - - + -
219B TYR* 3.8 39.9 - - + +
309B ALA 2.9 18.8 + - - +
310B ARG* 3.5 9.6 - - - +
311B ALA 3.3 0.2 - - - -
312B PHE* 1.3 77.1 - - - +
314B LYS* 1.3 55.9 + - - +
316B GLN* 3.3 6.1 + - - +
317B ALA* 2.9 28.1 + - - +
384B VAL* 3.8 37.9 - - + +
385B PHE* 4.0 19.6 - - + -
388B GLU* 4.0 20.4 - - + +
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Residues in contact with LYS 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296B ARG* 3.6 46.9 - - - +
310B ARG* 2.9 34.0 + - - +
311B ALA 3.6 4.9 - - - +
313B LEU* 1.3 76.1 - - - +
315B ALA* 1.3 56.8 + - - +
317B ALA* 3.4 2.6 + - - +
318B ALA* 2.9 27.9 + - - +
388B GLU* 2.5 48.4 + - - +
391B MET* 5.8 1.8 - - - +
393B GLU* 4.6 2.1 - - - +
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Residues in contact with ALA 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B TYR* 3.6 15.5 - - + +
289B VAL* 4.0 22.4 - - + +
293B LEU* 4.2 24.0 - - + -
311B ALA 3.1 13.4 + - - +
312B PHE* 3.5 7.9 - - - +
314B LYS* 1.3 75.1 - - - +
316B GLN* 1.3 65.0 + - - +
318B ALA* 3.2 2.3 + - - +
319B PHE* 2.9 27.9 + - - -
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Residues in contact with GLN 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B TYR* 2.5 32.6 + - - +
192B LEU* 3.9 4.3 - - - +
217B MET 3.9 8.7 - - - +
218B LEU* 2.9 33.3 + - - +
219B TYR 3.6 20.6 - - - +
220B PRO* 4.5 0.9 - - + -
221B MET* 4.1 9.9 - - - +
312B PHE 2.8 18.9 + - - +
313B LEU* 3.6 4.9 - - - +
315B ALA* 1.3 75.5 - - - +
317B ALA* 1.3 56.6 + - - +
319B PHE* 4.0 1.4 - - - -
320B PHE* 2.9 62.9 + - + +
363B LEU* 5.4 0.2 - - - +
385B PHE* 3.6 12.1 - - + -
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313B LEU 2.9 18.0 + - - +
314B LYS 3.6 5.2 - - - +
315B ALA 3.2 0.2 - - - -
316B GLN* 1.3 74.3 - - - +
318B ALA* 1.3 61.1 + - - +
321B GLY* 2.8 28.8 + - - -
385B PHE* 3.6 16.4 - - + -
388B GLU* 3.9 26.7 - - + -
389B ILE* 4.3 12.1 - - + +
393B GLU* 3.7 16.0 - - + +
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B VAL* 3.9 26.3 - - + +
314B LYS 2.9 18.0 + - - +
315B ALA 3.7 4.0 - - - +
317B ALA* 1.3 78.0 - - - +
319B PHE* 1.3 63.2 + - - +
321B GLY* 4.5 1.0 + - - -
322B SER 5.5 1.0 + - - -
351B MET* 4.1 10.7 - - - +
393B GLU* 3.6 23.1 + - - +
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Residues in contact with PHE 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188B TYR* 3.5 30.1 - + - -
192B LEU* 3.7 16.4 - - + -
285B LEU* 4.3 18.8 - - + -
286B PRO* 3.8 22.9 - - + -
289B VAL* 3.6 35.4 - - + -
290B ILE* 4.3 7.6 - - + -
315B ALA 2.9 18.7 + - - +
316B GLN* 4.0 2.0 - - - -
318B ALA* 1.3 78.7 - - - +
320B PHE* 1.3 68.9 + - + +
322B SER* 5.1 1.3 + - - -
351B MET* 3.5 30.0 - - - +
354B PHE* 3.5 38.3 - + + -
355B LEU* 4.0 8.3 - - - +
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Residues in contact with PHE 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192B LEU* 4.0 15.5 - - + -
221B MET* 3.7 28.5 - - + -
316B GLN* 2.9 51.8 + - - +
319B PHE* 1.3 84.8 - - + +
321B GLY* 1.3 66.6 + - - +
322B SER* 3.1 4.3 - - - -
323B TYR* 3.0 27.9 + - + +
342B PHE* 4.4 6.5 - + - -
354B PHE* 3.7 18.8 - + - -
358B ALA* 3.8 26.5 - - + -
361B LEU* 4.5 7.9 - - + -
363B LEU* 4.6 0.9 - - + -
364B PHE* 3.6 36.6 - + + -
385B PHE* 4.3 5.2 - - + -
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Residues in contact with GLY 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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316B GLN 4.0 0.4 + - - -
317B ALA* 2.8 22.9 + - - -
318B ALA 4.5 0.2 - - - -
319B PHE 3.7 0.6 - - - -
320B PHE* 1.3 78.9 - - - +
322B SER* 1.3 56.5 + - - +
323B TYR 3.0 5.8 + - - -
324B ARG* 3.7 7.6 + - - +
385B PHE* 4.5 0.2 - - - -
389B ILE* 3.6 38.9 - - - +
393B GLU* 4.1 10.3 - - - -
394B TYR* 4.0 6.2 - - - +
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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