Contacts of the helix formed by residues 339 - 354 (chain B) in PDB entry 1EKF
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 PRO 339 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179B VAL* 5.9 1.8 - - + -
307B GLU* 3.7 8.5 - - - +
319B PRO* 5.8 0.9 - - + -
334B THR* 3.8 10.1 - - + +
335B MET* 3.8 42.4 - - + +
337B ASN 2.7 6.1 - - - +
338B GLY* 1.3 76.2 - - - +
340B GLU* 1.3 52.5 + - - +
341B LEU 3.7 1.3 - - - -
342B ILE* 3.5 10.7 + - + -
343B LEU* 2.8 61.3 + - + +
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Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TYR* 5.5 0.4 - - + -
306B ARG* 3.3 27.0 + - - +
307B GLU* 3.2 9.0 + - - +
338B GLY* 2.3 31.6 + - - +
339B PRO 1.3 66.5 - - - +
341B LEU* 1.3 60.0 + - - +
343B LEU* 3.3 4.8 + - - +
344B ARG* 2.9 29.2 + - - +
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Residues in contact with LEU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B TYR* 3.5 45.7 - - + +
256B LEU* 3.9 23.8 - - + -
281B TRP* 3.5 33.4 - - + -
284B PHE* 4.2 7.0 - - + -
307B GLU* 2.7 22.6 + - - +
309B PHE* 4.6 4.5 - - + -
340B GLU* 1.3 71.0 - - - +
342B ILE* 1.3 64.8 + - - +
344B ARG* 3.1 5.6 + - + +
345B PHE* 2.8 43.4 + - + +
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Residues in contact with ILE 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 4.6 4.0 - - + -
307B GLU* 3.0 17.1 + - - +
309B PHE* 3.5 44.0 - - + -
317B VAL* 3.7 21.5 - - + +
319B PRO* 3.7 28.0 - - + -
334B THR* 3.7 23.3 - - + -
339B PRO* 3.8 9.0 - - + +
341B LEU* 1.3 76.3 - - - +
343B LEU* 1.3 65.8 + - + +
345B PHE* 3.2 3.3 + - - +
346B GLN* 2.9 47.6 + - - +
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Residues in contact with LEU 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B VAL* 4.8 15.5 - - + -
339B PRO* 2.8 57.6 + - + +
340B GLU* 3.8 5.4 - - - +
342B ILE* 1.3 74.1 - - + +
344B ARG* 1.3 62.8 + - - +
346B GLN* 3.5 20.4 + - - +
347B LYS* 3.1 23.4 + - - +
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Residues in contact with ARG 344 (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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281B TRP* 3.4 60.1 - - + +
283B GLU* 2.8 43.0 + - - -
284B PHE* 5.4 1.6 - - - -
340B GLU 2.9 17.3 + - - +
341B LEU* 3.1 7.5 + - + +
343B LEU* 1.3 76.5 - - - +
345B PHE* 1.3 62.9 + - - +
347B LYS* 3.4 7.0 + - - +
348B GLU* 3.0 28.7 + - + +
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Residues in contact with PHE 345 (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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256B LEU* 3.8 19.1 - - + -
274B LEU* 3.6 53.6 - - + -
277B MET* 3.9 14.1 - - + -
278B ALA* 4.0 4.5 - - + -
281B TRP* 3.4 26.9 - + - -
309B PHE* 4.0 24.7 - + - -
317B VAL* 4.0 15.3 - - + -
341B LEU* 2.8 43.2 + - + +
342B ILE 3.6 3.8 - - - +
344B ARG* 1.3 77.2 - - - +
346B GLN* 1.3 62.2 + - - +
348B GLU* 3.4 3.8 + - - +
349B LEU* 3.0 29.7 + - - +
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Residues in contact with GLN 346 (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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174B PHE* 4.0 8.3 - - - -
179B VAL* 3.3 37.0 - - - +
316B GLN* 5.9 3.2 - - + +
317B VAL* 3.1 42.8 + - + +
342B ILE* 2.9 27.2 + - - +
343B LEU* 3.8 16.8 - - + +
345B PHE* 1.3 75.7 - - - +
347B LYS* 1.3 57.6 + - - +
349B LEU* 3.5 5.0 + - - +
350B LYS* 2.9 33.1 + - - +
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Residues in contact with LYS 347 (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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343B LEU 3.1 15.3 + - - +
344B ARG* 3.7 7.0 - - - +
345B PHE 3.2 0.2 - - - -
346B GLN* 1.3 77.7 - - - +
348B GLU* 1.3 67.1 + - + +
350B LYS* 3.2 19.1 + - - +
351B GLU* 2.9 51.2 + - + +
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Residues in contact with GLU 348 (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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277B MET* 3.5 32.9 - - - +
281B TRP* 2.5 42.7 + - + -
344B ARG* 3.0 23.4 + - + +
345B PHE 3.9 0.2 - - - +
347B LYS* 1.3 75.7 - - - +
349B LEU* 1.3 62.2 + - - +
351B GLU* 3.3 16.1 + - - +
352B ILE* 3.0 38.7 + - - +
357B ARG* 5.3 8.2 + - - +
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Residues in contact with LEU 349 (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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91B PHE* 4.0 31.4 - - + -
270B VAL* 4.6 8.3 - - + -
273B SER* 5.0 4.0 - - - -
274B LEU* 4.2 18.8 - - + -
277B MET* 3.6 24.9 - - + -
316B GLN* 3.4 38.1 - - + +
317B VAL* 4.4 6.5 - - + -
345B PHE 3.0 20.2 + - - +
346B GLN* 3.9 4.5 - - - +
348B GLU* 1.3 74.0 - - - +
350B LYS* 1.3 58.0 + - - +
352B ILE* 3.2 3.0 + - + -
353B GLN* 2.7 43.2 + - - +
361B TRP* 4.5 1.8 - - + -
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Residues in contact with LYS 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B ALA* 6.6 0.2 - - + -
137B GLY 6.3 1.1 - - - +
346B GLN* 2.9 17.4 + - - +
347B LYS* 3.2 22.5 + - - +
349B LEU* 1.3 77.5 - - - +
351B GLU* 1.3 65.6 + - - +
353B GLN* 4.6 3.1 - - - -
354B TYR* 3.0 53.3 + - + +
356B ILE* 4.7 1.9 - - + +
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Residues in contact with GLU 351 (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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347B LYS* 2.9 45.2 + - + +
348B GLU* 3.6 16.2 - - - +
350B LYS* 1.3 80.6 - - + +
352B ILE* 1.3 61.0 + - - +
355B GLY 3.5 0.2 + - - -
356B ILE* 2.9 49.4 + - + +
357B ARG* 3.1 55.5 + - + -
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Residues in contact with ILE 352 (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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91B PHE* 4.6 4.0 - - + -
277B MET* 3.9 25.1 - - + -
348B GLU* 3.0 27.2 + - - +
349B LEU* 3.7 5.2 - - + +
351B GLU* 1.3 79.2 - - + +
353B GLN* 1.3 63.7 + - + +
355B GLY* 3.2 12.1 + - - -
357B ARG* 4.0 16.2 - - + +
359B HIS* 3.7 46.4 - - + +
361B TRP* 4.1 18.4 - - + -
362B MET* 3.3 31.7 - - + +
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Residues in contact with GLN 353 (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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81B PHE* 3.3 59.6 - - + +
89B ARG* 4.6 3.6 + - - -
91B PHE* 3.7 40.6 - - + -
316B GLN* 2.8 42.4 + - - +
349B LEU* 2.7 28.3 + - - +
350B LYS* 4.4 2.9 + - - -
352B ILE* 1.3 72.3 - - - +
354B TYR* 1.3 64.7 + - + +
355B GLY 3.3 0.7 + - - -
362B MET* 3.5 16.7 - - - +
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Residues in contact with TYR 354 (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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81B PHE* 3.5 35.2 - + + -
82B LYS 3.6 23.8 - - - -
83B GLY* 3.7 21.2 - - - -
84B LYS* 3.8 12.7 - - + +
89B ARG* 3.9 5.4 + - - -
133B PRO 5.9 0.4 - - - -
134B ASP* 5.9 2.2 - - - -
135B ALA 4.9 7.0 - - - -
136B ALA* 5.7 1.6 - - - -
137B GLY* 3.7 15.1 - - - -
138B THR 2.6 37.6 + - - -
350B LYS* 3.0 41.9 + - + +
353B GLN* 1.3 79.8 - - + +
355B GLY* 1.3 61.9 + - - +
356B ILE* 3.3 11.4 + - + +
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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