Contacts of the helix formed by residues 317 - 335 (chain T) 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 VAL 317 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227T GLU* 5.6 0.4 - - - -
258T MET* 3.5 8.9 - - - +
315T ALA* 3.3 16.6 - - - +
316T LYS* 1.3 85.4 - - + +
318T ARG* 1.3 64.1 + - - +
319T ALA* 3.9 12.6 - - + +
320T GLU* 3.3 39.2 + - + +
321T ILE* 3.8 0.9 + - - +
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Residues in contact with ARG 318 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165T LEU* 3.4 36.6 - - + +
225T LYS 4.9 0.4 + - - -
226T SER* 4.6 11.9 - - - -
227T GLU* 3.1 30.9 + - - +
258T MET* 3.7 15.7 - - + -
317T VAL* 1.3 74.7 - - - +
319T ALA* 1.3 61.6 + - - +
321T ILE* 3.1 7.9 + - - +
322T TYR* 3.0 63.6 + - + -
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Residues in contact with ALA 319 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317T VAL* 3.2 12.6 - - + +
318T ARG* 1.3 80.0 - - - +
320T GLU* 1.3 56.2 + - + +
322T TYR* 3.9 9.2 - - - +
323T GLU* 2.8 35.6 + - - +
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Residues in contact with GLU 320 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298T PRO* 3.4 31.2 - - + +
299T ARG 5.1 2.3 + - - +
300T ILE* 3.9 8.4 - - + +
314T GLY 4.4 1.7 - - - +
315T ALA* 3.3 11.6 - - + -
316T LYS* 3.2 32.4 + - - +
317T VAL* 3.3 24.1 + - + +
318T ARG 3.2 0.8 - - - -
319T ALA* 1.3 76.7 - - + +
321T ILE* 1.3 59.3 + - - +
323T GLU* 4.4 2.5 - - - +
324T ALA* 2.9 31.7 + - - +
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Residues in contact with ILE 321 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163T PRO* 4.0 25.4 - - + -
165T LEU* 4.7 20.9 - - + -
258T MET* 4.3 15.3 - - + +
260T GLY* 4.6 5.6 - - - +
300T ILE* 4.7 5.2 - - + -
312T LEU* 3.3 50.2 - - + +
313T THR* 4.3 1.3 - - - +
315T ALA* 3.7 25.4 - - + -
317T VAL 3.8 4.0 + - - +
318T ARG* 3.1 8.8 + - - +
320T GLU* 1.3 76.6 - - - +
322T TYR* 1.3 65.8 + - + +
324T ALA* 3.3 1.2 + - - -
325T PHE* 3.0 21.0 + - - +
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Residues in contact with TYR 322 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162T VAL* 4.0 17.5 - - + +
163T PRO* 3.6 47.1 + - + -
165T LEU* 5.8 1.3 - - + -
318T ARG* 3.0 62.5 + - + +
319T ALA* 4.0 7.0 - - - +
321T ILE* 1.3 79.5 - - + +
323T GLU* 1.3 57.4 + - - +
325T PHE* 3.4 2.6 + - - +
326T GLU* 3.0 36.5 + - + +
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Residues in contact with GLU 323 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297T LYS* 4.3 21.4 + - - +
298T PRO* 3.7 21.8 - - + +
319T ALA* 2.8 21.3 + - - +
320T GLU* 4.0 6.2 - - - +
322T TYR* 1.3 76.9 - - - +
324T ALA* 1.3 58.4 + - - +
326T GLU* 3.4 5.1 + - - +
327T ASN* 2.8 49.2 + - - +
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Residues in contact with ALA 324 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295T MET* 3.4 24.4 - - + +
298T PRO* 4.2 1.5 - - + +
300T ILE* 3.7 28.3 - - + -
302T LEU* 4.6 1.8 - - + -
312T LEU* 3.8 13.5 - - + -
320T GLU 2.9 20.1 + - - +
321T ILE 3.3 4.2 + - - +
323T GLU* 1.3 76.8 - - - +
325T PHE* 1.3 57.5 + - - +
327T ASN 3.4 0.3 + - - -
328T ILE* 3.0 29.7 + - - +
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Residues in contact with PHE 325 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159T SER* 3.9 11.2 - - - -
161T ILE* 3.5 46.2 - - + -
163T PRO* 3.8 23.3 - - + -
262T CYS* 3.5 22.0 - - - -
264T VAL* 3.6 21.1 - - + -
310T VAL* 4.9 5.8 - - + -
312T LEU* 3.5 13.8 - - + +
321T ILE 3.0 16.8 + - - +
322T TYR 4.0 2.0 - - - +
324T ALA* 1.3 77.3 - - - +
326T GLU* 1.3 64.8 + - + +
328T ILE* 3.9 11.4 - - + -
329T TYR* 3.0 57.1 + + + +
332T LEU* 4.9 2.5 - - + -
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Residues in contact with GLU 326 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159T SER* 3.9 33.2 + - - +
161T ILE 4.8 2.8 - - - +
322T TYR* 3.0 23.7 + - + +
323T GLU* 3.9 6.5 - - - +
325T PHE* 1.3 85.0 - - + +
327T ASN* 1.3 62.5 + - - +
329T TYR* 4.4 7.3 - - - +
330T PRO* 3.3 18.0 - - - +
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Residues in contact with ASN 327 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295T MET* 3.7 14.0 - - + -
297T LYS 3.4 23.1 + - - -
298T PRO* 3.8 2.4 - - - +
323T GLU* 2.8 44.9 + - - +
324T ALA 3.7 4.0 - - - +
325T PHE 3.2 0.2 - - - -
326T GLU* 1.3 79.5 - - - +
328T ILE* 1.3 62.9 + - - +
330T PRO* 3.4 15.8 - - - +
331T ILE* 4.4 7.3 - - - +
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Residues in contact with ILE 328 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273T LEU* 5.7 3.4 - - + -
293T TYR* 3.6 38.6 - - + -
295T MET* 4.0 7.2 - - + -
302T LEU* 3.7 25.6 - - + -
304T ILE* 4.1 20.0 - - + -
310T VAL* 5.1 0.4 - - + -
324T ALA 3.0 19.8 + - - +
325T PHE* 3.6 15.3 - - + +
327T ASN* 1.3 77.6 - - - +
329T TYR* 1.3 66.5 + - - +
331T ILE* 3.1 15.1 + - + +
332T LEU* 3.1 42.2 + - + +
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Residues in contact with TYR 329 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159T SER* 3.5 35.4 - - - -
161T ILE* 5.3 4.8 - - + +
264T VAL* 4.0 17.5 + - + -
266T PHE* 4.0 26.1 - + - -
325T PHE* 3.0 42.9 + + + +
326T GLU* 4.4 7.9 - - - +
328T ILE* 1.3 77.4 - - - +
330T PRO* 1.4 64.5 - - + +
332T LEU* 3.2 9.4 + - + +
333T LYS* 2.9 63.4 + - + +
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Residues in contact with PRO 330 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326T GLU 3.3 19.3 - - - +
327T ASN* 3.4 12.1 - - - +
329T TYR* 1.4 91.5 - - + +
331T ILE* 1.3 64.8 + - + +
333T LYS* 3.4 21.2 + - - +
334T GLY* 2.9 23.7 + - - -
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Residues in contact with ILE 331 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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273T LEU* 3.9 18.2 - - + -
277T HIS* 3.9 36.6 - - + +
293T TYR* 5.8 6.5 - - + +
327T ASN 4.4 10.3 - - - +
328T ILE* 3.1 17.4 + - + +
330T PRO* 1.3 80.8 - - + +
332T LEU* 1.3 59.9 + - + +
334T GLY* 3.1 4.0 + - - -
335T PHE* 3.0 32.4 + - + +
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Residues in contact with LEU 332 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264T VAL* 4.2 18.2 - - + -
266T PHE* 3.2 17.9 - - + -
268T ILE* 3.7 45.8 - - + +
273T LEU* 4.7 10.8 - - + -
304T ILE* 4.5 6.7 - - + -
310T VAL* 4.2 12.3 - - + -
325T PHE* 4.9 0.7 - - + -
328T ILE* 3.1 47.3 + - + +
329T TYR* 3.2 10.3 + - - +
331T ILE* 1.3 78.2 - - + +
333T LYS* 1.3 64.6 + - - +
335T PHE* 3.1 14.5 + - + +
336T ARG 3.2 10.0 + - - -
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Residues in contact with LYS 333 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266T PHE* 3.9 15.0 - - + -
329T TYR* 2.9 56.3 + - + +
330T PRO* 3.6 21.3 - - - +
332T LEU* 1.3 76.0 - - - +
334T GLY* 1.3 59.7 + - - +
335T PHE 3.3 0.5 + - - -
336T ARG* 3.5 19.3 - - - +
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Residues in contact with GLY 334 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269T ARG* 3.3 9.9 + - - -
330T PRO 2.9 14.6 + - - -
331T ILE* 3.1 6.1 + - - -
333T LYS* 1.3 75.1 - - - +
335T PHE* 1.3 72.1 + - - +
336T ARG 3.6 1.2 + - - -
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Residues in contact with PHE 335 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268T ILE* 3.4 9.5 - - + -
269T ARG* 3.0 65.7 + - + +
272T GLY* 4.4 4.9 - - - -
273T LEU* 3.6 42.6 - - + -
276T THR* 3.3 33.7 - - + -
277T HIS* 3.9 11.4 - + - -
331T ILE* 3.0 21.0 + - + +
332T LEU* 3.1 7.1 + - + +
334T GLY* 1.3 90.5 - - - +
336T ARG* 1.3 62.1 + - - +
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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
------------------------------------------------------------
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