Contacts of the helix formed by residues 313 - 327 (chain T) in PDB entry 3MQT
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 THR 313 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26T THR* 4.1 2.9 - - - +
42T GLU* 3.0 22.9 + - - +
310T ASN* 5.1 1.4 - - - +
312T LYS* 1.3 84.3 + - - +
314T GLY* 1.3 72.3 + - - +
315T ILE* 3.0 17.8 + - + +
316T THR* 3.4 2.8 + - - -
317T ALA* 3.1 22.9 + - - +
345T LEU* 3.6 34.1 - - - +
346T THR* 5.4 2.5 - - - +
349T LEU* 2.8 38.1 - - + +
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Residues in contact with GLY 314 (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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313T THR* 1.3 77.3 - - - +
315T ILE* 1.3 57.8 + - - -
317T ALA* 3.6 13.2 - - - +
318T ALA* 3.0 27.0 + - - +
321T ARG* 4.7 0.5 + - - -
345T LEU 5.1 4.2 + - - -
346T THR* 5.5 4.4 + - - +
349T LEU* 5.3 0.4 - - - +
350T THR* 3.8 29.9 + - - +
353T GLU* 4.1 8.7 - - - +
371T ILE* 4.6 1.4 - - - +
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Residues in contact with ILE 315 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28T ILE* 4.0 33.9 - - + -
40T LEU* 4.0 9.2 - - + +
41T GLY* 3.7 35.0 - - - +
42T GLU* 3.6 14.6 - - + +
107T MET* 4.0 4.5 - - - +
313T THR* 3.0 11.4 - - + +
314T GLY* 1.3 75.3 - - - +
316T THR* 1.3 62.3 + - - +
318T ALA* 3.3 7.3 + - - +
319T ALA* 3.3 17.7 + - - +
349T LEU* 4.0 19.5 - - + -
350T THR* 4.9 0.4 - - + -
369T LEU* 4.4 1.3 - - + +
371T ILE* 3.9 33.4 - - + +
373T LEU* 4.7 6.5 - - + -
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Residues in contact with THR 316 (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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42T GLU* 2.6 38.0 + - - +
107T MET* 3.8 5.9 - - - +
283T TYR* 3.7 26.7 - - + -
284T ASN* 3.0 25.1 + - - +
309T HIS 5.3 0.2 - - - +
310T ASN* 3.5 20.2 - - - +
312T LYS* 4.0 5.6 - - + -
313T THR 3.4 3.8 + - - -
315T ILE* 1.3 71.8 - - - +
317T ALA* 1.3 60.0 + - - +
319T ALA* 3.1 7.1 + - - +
320T ALA* 2.8 26.9 + - - +
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Residues in contact with ALA 317 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310T ASN* 4.4 7.5 + - - +
313T THR 3.1 9.3 + - - +
314T GLY* 3.6 20.0 - - - +
315T ILE 3.3 0.4 - - - -
316T THR* 1.3 76.5 - - - +
318T ALA* 1.3 63.0 + - - +
320T ALA* 3.1 9.1 + - - +
321T ARG* 3.0 31.4 + - - +
335T TYR* 3.7 25.2 - - + +
336T LEU* 4.7 9.6 - - + +
353T GLU* 4.2 4.0 - - - +
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Residues in contact with ALA 318 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314T GLY 3.0 10.0 + - - +
315T ILE 3.6 8.7 - - - +
317T ALA* 1.3 75.3 - - - +
319T ALA* 1.3 62.2 + - - +
321T ARG* 3.3 24.7 + - - +
322T HIS* 3.2 30.5 + - - -
369T LEU* 3.5 27.1 - - + +
371T ILE* 3.6 20.9 - - + -
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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
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107T MET* 4.0 36.1 - - + -
125T MET* 4.7 2.5 - - - +
283T TYR* 4.3 13.2 - - + -
289T VAL* 4.9 8.9 - - + +
315T ILE 3.3 3.9 + - - +
316T THR* 3.1 10.8 + - - +
318T ALA* 1.3 75.4 - - - +
320T ALA* 1.3 57.0 + - - +
322T HIS* 3.3 1.9 + - - +
323T PHE* 2.9 32.2 + - - +
369T LEU* 4.0 15.2 - - + +
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Residues in contact with ALA 320 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133T LEU* 4.3 2.0 - - - +
283T TYR* 3.3 29.3 + - + +
310T ASN* 3.4 28.3 - - - +
316T THR 2.8 9.8 + - - +
317T ALA* 3.5 7.4 - - - +
319T ALA* 1.3 74.3 - - - +
321T ARG* 1.3 59.6 + - - +
323T PHE* 4.6 0.2 - - - -
324T GLY* 2.8 27.7 + - - -
333T VAL* 4.3 7.1 - - + +
334T GLU 4.4 4.7 - - - +
335T TYR* 4.5 6.3 - - + -
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Residues in contact with ARG 321 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133T LEU* 3.6 11.6 - - + +
314T GLY 4.9 0.6 + - - -
317T ALA* 3.0 14.4 + - - +
318T ALA* 3.6 37.0 + - - +
320T ALA* 1.3 76.0 - - - +
322T HIS* 1.3 64.8 + - + +
324T GLY* 3.9 0.2 - - - -
325T ILE* 3.1 18.7 + - - +
335T TYR* 2.9 26.1 + - + -
353T GLU* 3.1 23.2 + - - -
354T PRO* 3.7 19.1 - - - +
361T ILE* 2.9 32.5 - - + -
362T GLU 4.1 7.3 + - - -
363T VAL* 3.5 31.9 - - + +
364T SER 5.7 1.2 - - - +
369T LEU 4.6 3.0 + - - -
370T GLY 4.4 13.5 + - - -
371T ILE* 5.4 1.2 - - - +
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Residues in contact with HIS 322 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120T PRO* 3.8 6.7 - - + -
121T ALA* 3.4 11.4 + - + -
122T TYR* 2.9 40.6 + + - +
125T MET* 3.7 23.6 - - + -
318T ALA* 3.2 23.7 + - - +
319T ALA 3.8 1.1 - - - +
321T ARG* 1.3 80.3 - - + +
323T PHE* 1.3 65.0 + - - +
325T ILE* 3.2 20.3 - - - +
326T VAL* 3.4 9.7 + - - +
363T VAL* 4.2 9.8 - - + +
364T SER* 3.9 13.0 + - - -
366T LYS 4.7 0.8 + - - -
368T GLY 3.3 19.0 + - - -
369T LEU* 3.4 31.7 + - + -
370T GLY* 5.0 0.6 - - - -
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Residues in contact with PHE 323 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125T MET* 3.6 12.0 - - + -
283T TYR* 3.8 28.0 - + + -
289T VAL* 4.6 13.7 - - + -
292T LEU* 3.9 24.5 - - + -
293T LEU* 4.1 28.0 - - + -
296T MET* 4.6 5.6 - - - -
306T LEU* 3.5 25.8 - - + -
308T PRO* 3.7 21.5 - - + -
319T ALA 2.9 17.5 + - - +
320T ALA 4.4 0.2 - - - +
322T HIS* 1.3 75.0 - - - +
324T GLY* 1.3 60.5 + - - +
326T VAL* 2.9 7.9 + - + +
327T CYS* 2.9 49.6 + - + +
333T VAL* 5.1 1.3 - - + -
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Residues in contact with GLY 324 (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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130T LYS* 3.1 28.1 + - - +
133T LEU* 3.6 17.5 - - - -
320T ALA 2.8 24.6 + - - -
323T PHE* 1.3 75.4 - - - +
325T ILE* 1.3 57.8 + - - +
327T CYS* 3.4 7.3 + - - +
333T VAL* 4.4 18.4 - - - -
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Residues in contact with ILE 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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122T TYR* 3.6 30.7 - - + -
128T ALA* 4.1 15.3 - - + -
129T GLN 2.9 22.5 + - - -
130T LYS* 3.4 34.7 - - + +
131T ALA 4.7 2.0 - - - +
132T GLN* 3.8 5.4 - - - +
133T LEU* 3.7 29.3 - - + +
321T ARG 3.1 15.5 + - - +
322T HIS* 3.2 18.2 - - - +
323T PHE 3.3 0.2 - - - -
324T GLY* 1.3 75.3 - - - +
326T VAL* 1.3 59.7 + - - +
363T VAL* 3.9 21.5 - - + -
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Residues in contact with VAL 326 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122T TYR* 3.5 24.9 - - + +
125T MET* 3.7 28.3 - - + +
127T GLY 3.3 23.8 - - - +
129T GLN* 3.5 21.1 - - - +
293T LEU* 4.1 17.3 - - + -
296T MET* 4.3 10.0 - - + +
322T HIS 3.5 13.0 - - - +
323T PHE* 2.9 12.0 + - + +
325T ILE* 1.3 80.5 - - - +
327T CYS* 1.3 58.1 + - - +
328T HIS* 2.9 11.4 + - - -
79X ARG* 5.2 1.6 - - - -
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Residues in contact with CYS 327 (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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130T LYS* 3.2 19.2 + - - -
296T MET* 3.8 19.7 - - - -
306T LEU* 4.0 9.2 - - - -
323T PHE* 2.9 42.7 + - + +
324T GLY* 3.4 8.4 + - - +
326T VAL* 1.3 72.7 - - - +
328T HIS* 1.3 63.1 + - - +
329T ILE* 3.2 18.4 - - - -
330T SER* 3.2 30.1 + - - +
333T VAL* 5.1 2.2 - - + -
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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
------------------------------------------------------------
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