Contacts of the helix formed by residues 257 - 270 (chain C) in PDB entry 5MLE
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 257 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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229C GLU* 3.5 41.7 + - - +
232C GLU* 2.7 23.4 + - - -
255C VAL* 4.3 0.2 - - - +
256C MET* 1.3 79.7 - - - +
258C LYS* 1.3 66.8 + - - +
259C SER* 4.1 0.7 + - - -
260C SER* 3.3 17.2 + - - -
261C ALA* 3.2 23.4 + - - +
308C SER* 5.0 3.6 - - - -
313C THR* 4.1 6.3 - - - -
317C LEU* 3.7 5.4 - - - +
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Residues in contact with LYS 258 (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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229C GLU* 3.9 9.2 + - - +
257C SER* 1.3 69.8 - - - +
259C SER* 1.3 55.3 + - - +
261C ALA* 3.1 4.0 + - - +
262C GLU* 2.8 37.8 + - - +
310C ASP* 3.1 17.5 + - - -
312C THR* 2.7 30.9 + - - +
313C THR* 3.9 18.6 - - + +
316C PHE* 3.5 56.1 - - + -
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Residues in contact with SER 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229C GLU* 2.8 30.5 + - - +
230C GLU* 5.3 3.8 + - - +
233C ALA* 3.6 19.3 - - - -
257C SER* 4.2 3.8 - - - -
258C LYS* 1.3 76.1 - - - +
260C SER* 1.3 56.8 + - - +
262C GLU* 3.4 6.5 + - - +
263C VAL* 3.0 32.4 + - - +
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Residues in contact with SER 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C GLU* 2.8 43.4 + - - -
233C ALA* 4.0 11.0 - - - +
236C VAL* 4.0 16.1 - - - +
252C ILE* 6.0 0.2 - - - -
255C VAL* 3.7 9.3 - - - +
257C SER* 3.3 13.5 + - - -
258C LYS 3.2 1.0 - - - -
259C SER* 1.3 76.1 - - - +
261C ALA* 1.3 67.4 + - - +
263C VAL* 3.3 7.2 + - - +
264C ILE* 3.1 28.0 + - - +
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Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
255C VAL* 4.1 12.6 - - + -
257C SER 3.2 14.7 + - - +
258C LYS 3.1 4.6 + - - +
260C SER* 1.3 81.1 + - - +
262C GLU* 1.3 57.2 + - - +
264C ILE* 3.1 9.1 + - - +
265C ALA* 2.9 28.1 + - - +
316C PHE* 4.5 0.9 - - + -
317C LEU* 3.6 22.0 - - + -
320C LEU* 3.8 20.9 - - + +
325C ASP 5.5 0.2 - - - +
326C LEU* 4.2 9.1 - - + +
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Residues in contact with GLU 262 (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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258C LYS 2.8 21.0 + - - +
259C SER* 3.7 7.4 - - - +
260C SER 3.2 0.2 - - - -
261C ALA* 1.3 72.3 - - - +
263C VAL* 1.3 63.5 + - + +
265C ALA* 3.1 14.2 + - - +
266C GLN* 3.0 54.5 + - + +
316C PHE* 4.4 18.6 - - + -
320C LEU* 4.6 4.4 - - - +
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Residues in contact with VAL 263 (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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233C ALA* 4.3 17.7 - - + +
236C VAL* 4.2 4.7 - - + -
237C ASN* 4.0 32.1 - - + +
240C ILE* 3.9 22.4 - - + -
259C SER 3.0 18.8 + - - +
260C SER* 3.3 8.9 + - - +
262C GLU* 1.3 76.9 - - - +
264C ILE* 1.3 61.1 + - - +
266C GLN* 3.5 6.9 + - - +
267C ALA* 3.2 22.2 + - + +
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Residues in contact with ILE 264 (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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236C VAL* 4.0 14.4 - - + -
240C ILE* 5.0 1.6 - - + -
252C ILE* 3.8 28.9 - - + -
255C VAL* 3.9 26.2 - - + -
260C SER* 3.1 18.9 + - - +
261C ALA* 3.5 6.3 - - - +
263C VAL* 1.3 71.5 - - - +
265C ALA* 1.3 67.3 + - - +
267C ALA* 3.4 6.0 + - - +
268C ARG* 3.1 33.7 + - + +
274C VAL* 4.3 18.1 - - + +
275C TYR 4.7 1.1 - - - -
276C GLY* 4.1 15.5 - - - +
325C ASP 4.0 17.3 - - - +
326C LEU* 4.4 8.7 - - + -
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Residues in contact with ALA 265 (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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261C ALA 2.9 13.1 + - - +
262C GLU* 3.1 23.5 + - - +
264C ILE* 1.3 78.4 - - - +
266C GLN* 1.3 64.5 + - - +
268C ARG* 3.2 10.5 + - - +
269C LYS* 3.2 24.8 + - + +
320C LEU* 4.6 4.0 - - + -
325C ASP* 4.1 36.6 + - + +
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Residues in contact with GLN 266 (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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262C GLU* 3.0 39.9 + - + +
263C VAL* 3.8 6.7 - - - +
265C ALA* 1.3 77.7 - - - +
267C ALA* 1.3 62.6 + - - +
269C LYS* 3.4 36.1 + - - +
270C LYS* 3.5 28.1 + - + +
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Residues in contact with ALA 267 (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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240C ILE* 4.2 18.4 - - + -
263C VAL* 3.2 16.2 + - + +
264C ILE 3.8 4.5 - - - +
265C ALA 3.3 0.2 - - - -
266C GLN* 1.3 79.9 - - - +
268C ARG* 1.3 61.0 + - - +
270C LYS* 3.3 13.5 + - - +
271C GLY 3.5 0.3 + - - -
272C THR* 3.0 44.5 + - + +
274C VAL* 4.2 9.2 - - + -
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Residues in contact with ARG 268 (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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264C ILE* 3.1 17.5 + - - +
265C ALA* 3.2 8.7 + - - +
267C ALA* 1.3 75.8 - - - +
269C LYS* 1.3 56.9 + - + +
271C GLY* 2.7 25.5 + - - -
272C THR 4.0 1.8 - - - -
274C VAL* 3.0 32.8 + - + -
275C TYR* 3.9 18.6 - - - -
324C GLY 3.8 8.1 + - - -
325C ASP* 3.7 15.7 - - - +
327C GLN* 3.3 37.1 - - - +
477C PHE* 5.8 2.8 - - - -
481C ARG* 3.6 50.7 + - - +
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Residues in contact with LYS 269 (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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265C ALA* 3.2 21.0 + - - +
266C GLN* 3.4 24.4 + - - +
267C ALA 3.3 0.4 - - - -
268C ARG* 1.3 76.9 - - + +
270C LYS* 1.3 59.1 + - + +
271C GLY 3.3 0.9 + - - -
325C ASP* 4.7 15.0 - - - +
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Residues in contact with LYS 270 (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 SER* 5.9 1.8 + - - -
262A GLU* 5.7 2.8 + - - -
266C GLN* 3.5 23.4 + - - +
267C ALA* 3.3 11.8 + - - +
268C ARG 3.1 0.6 - - - -
269C LYS* 1.3 78.7 - - + +
271C GLY* 1.3 58.6 + - - +
272C THR* 3.4 5.9 + - - +
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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