Contacts of the helix formed by residues 257 - 274 (chain I) in PDB entry 6MZL
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 257 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347H THR 5.8 1.8 - - - +
348H THR* 5.8 9.2 - - + -
349H ASN* 4.6 11.2 - - - +
253I TYR 5.0 2.2 - - - +
254I GLN* 5.7 0.9 - - - +
256I LEU* 1.3 85.2 - - + +
258I ARG* 1.4 51.2 + - - +
259I PHE 3.2 1.3 - - - -
260I SER* 2.6 19.7 + - - +
261I THR* 2.4 47.4 + - - +
300I TYR* 3.5 48.7 - - + +
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Residues in contact with ARG 258 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221I GLN* 4.8 13.3 + - - +
224I TYR* 4.2 9.8 + - - +
254I GLN 6.0 0.2 - - - +
255I MET* 6.2 3.1 - - - +
256I LEU 2.6 13.1 + - - +
257I PRO* 1.4 70.7 - - - +
259I PHE* 1.3 63.3 + - - +
261I THR* 3.7 6.7 - - - -
262I PHE* 3.1 50.9 + - + -
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Residues in contact with PHE 259 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224I TYR* 3.4 40.3 + + + -
227I ILE* 3.9 17.3 - - + -
228I THR* 5.6 0.9 - - + -
246I ILE* 5.1 6.7 - - + -
255I MET* 3.1 31.2 - - + +
256I LEU* 3.7 10.3 + - + +
258I ARG* 1.3 76.9 - - - +
260I SER* 1.3 74.0 + - - +
262I PHE 3.9 0.2 - - - -
263I ILE* 2.9 45.3 + - + +
285I MET* 3.5 28.7 - - + -
289I LEU* 3.5 42.2 - - + -
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Residues in contact with SER 260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256I LEU* 4.6 7.9 - - - +
257I PRO* 2.6 33.5 + - - +
259I PHE* 1.3 92.7 - - - +
261I THR* 1.3 56.7 + - - -
263I ILE* 3.3 12.1 - - - +
264I SER* 2.9 33.0 + - - -
289I LEU* 5.2 6.5 - - - -
300I TYR* 5.2 4.2 + - - +
304I LEU* 3.7 28.0 - - - +
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Residues in contact with THR 261 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346H THR* 5.8 10.1 - - + +
349H ASN* 5.5 1.9 + - - -
257I PRO* 2.4 44.2 + - - +
258I ARG* 3.7 7.6 - - - -
260I SER* 1.3 73.1 + - - +
262I PHE* 1.3 67.5 + - + +
264I SER* 3.0 21.1 + - - -
265I GLU* 3.0 11.2 + - + +
303I GLU* 3.6 27.1 + - - +
304I LEU* 5.5 1.3 - - - -
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Residues in contact with PHE 262 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224I TYR* 3.8 28.0 - + - -
258I ARG* 3.1 36.6 + - + -
261I THR* 1.3 83.7 - - + +
263I ILE* 1.3 58.1 + - - +
265I GLU* 3.6 18.4 - - + -
266I GLY* 2.9 21.7 + - - -
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Residues in contact with ILE 263 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224I TYR* 5.5 2.2 + - - +
228I THR* 6.3 3.1 - - + -
259I PHE* 2.9 61.5 + - + +
260I SER* 3.3 12.3 - - - +
261I THR 3.2 0.2 - - - -
262I PHE* 1.3 76.4 - - - +
264I SER* 1.3 61.4 + - - +
266I GLY* 3.2 3.2 + - - -
267I VAL* 2.9 33.9 + - + +
282I LEU* 3.7 28.1 - - + +
285I MET* 3.7 18.4 - - + -
286I VAL* 5.3 12.3 - - + -
289I LEU* 5.0 4.0 - - + -
304I LEU* 6.0 0.9 - - + -
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Residues in contact with SER 264 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260I SER 2.9 14.4 + - - -
261I THR* 3.0 9.6 + - - -
263I ILE* 1.3 77.4 - - - +
265I GLU* 1.3 62.6 + - - +
267I VAL* 3.2 13.2 + - - +
268I ARG* 3.0 27.7 + - - +
303I GLU* 2.7 29.3 + - - -
304I LEU* 3.5 11.6 - - - +
307I ALA* 4.2 10.9 - - - +
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Residues in contact with GLU 265 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261I THR* 3.0 9.1 + - + +
262I PHE* 3.6 24.5 - - + -
264I SER* 1.3 78.8 - - - +
266I GLY* 1.3 56.3 + - - +
268I ARG* 3.2 30.8 + - - +
269I VAL* 3.0 44.7 + - + +
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Residues in contact with GLY 266 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262I PHE 2.9 16.1 + - - -
263I ILE* 3.6 4.0 - - - -
265I GLU* 1.3 72.1 - - - +
267I VAL* 1.3 59.1 + - - +
269I VAL* 3.8 6.0 - - - -
270I ASN* 2.9 44.3 + - - -
282I LEU* 4.6 4.9 - - - -
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Residues in contact with VAL 267 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263I ILE* 2.9 24.3 + - + +
264I SER* 3.2 14.8 + - - +
266I GLY* 1.3 77.1 - - - +
268I ARG* 1.3 59.7 + - + +
270I ASN* 3.6 2.6 - - - +
271I VAL* 2.8 40.5 + - + +
279I LEU* 5.3 4.9 - - + +
282I LEU* 3.7 27.6 - - + -
283I MET* 4.5 8.1 - - + -
307I ALA* 3.7 35.7 - - + +
310I THR* 5.4 1.6 - - - -
311I CYS* 4.1 13.2 - - - -
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Residues in contact with ARG 268 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264I SER* 3.0 17.2 + - - +
265I GLU* 3.2 32.6 + - - +
267I VAL* 1.3 79.3 - - + +
269I VAL* 1.3 63.0 + - + +
271I VAL* 3.2 11.6 + - - +
272I VAL* 3.1 26.2 + - - +
306I PRO* 6.1 3.6 - - - +
307I ALA* 6.2 2.0 - - + -
310I THR* 6.1 4.9 - - + -
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Residues in contact with VAL 269 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265I GLU* 3.0 31.1 + - + +
266I GLY* 4.0 6.7 - - - +
268I ARG* 1.3 75.8 - - + +
270I ASN* 1.3 66.6 + - - +
272I VAL* 3.3 12.2 - - + +
273I GLN* 2.9 29.5 + - + +
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Residues in contact with ASN 270 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266I GLY* 2.9 28.4 + - - +
267I VAL* 3.6 2.9 - - - +
269I VAL* 1.3 81.1 - - - +
271I VAL* 1.3 56.6 + - - +
272I VAL 3.2 0.4 - - - -
273I GLN* 3.4 18.6 - - + +
274I ASN* 2.5 31.0 + - - -
275I ASN* 3.5 8.0 + - + +
278I LEU* 3.5 44.2 - - + +
279I LEU* 5.3 7.8 - - + +
282I LEU* 4.9 6.5 - - + +
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Residues in contact with VAL 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267I VAL* 2.8 28.1 + - + +
268I ARG* 3.2 12.1 + - - +
270I ASN* 1.3 75.4 - - - +
272I VAL* 1.3 65.3 + - + +
274I ASN* 3.3 17.4 + - - +
279I LEU* 4.9 13.2 - - + -
310I THR* 3.8 38.4 - - + +
311I CYS* 5.3 1.3 - - - +
314I SER 5.9 2.2 - - - +
315I ARG 5.4 1.2 - - - +
316I GLN* 6.2 2.7 - - + +
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Residues in contact with VAL 272 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268I ARG 3.1 14.7 + - - +
269I VAL* 3.3 11.9 - - + +
271I VAL* 1.3 80.4 - - + +
273I GLN* 1.3 73.4 + - - +
274I ASN* 3.4 4.7 + - - +
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Residues in contact with GLN 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269I VAL* 2.9 26.4 + - + +
270I ASN* 3.2 21.7 + - + +
272I VAL* 1.3 86.3 - - - +
274I ASN* 1.3 71.3 + - - +
275I ASN* 3.6 8.5 - - + +
278I LEU* 5.9 0.2 - - + -
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Residues in contact with ASN 274 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270I ASN 2.5 17.3 + - - -
271I VAL* 3.6 11.7 - - - +
272I VAL 3.2 5.2 - - - +
273I GLN* 1.3 77.6 - - - +
275I ASN* 1.3 56.6 + - - +
279I LEU* 5.4 2.4 - - - +
315I ARG 3.0 21.4 + - - -
316I GLN* 3.2 9.2 - - - +
317I LEU* 2.6 49.5 + - - +
318I CYS* 3.2 18.7 + - - +
326I HIS* 4.8 0.5 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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