Contacts of the helix formed by residues 313 - 327 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26F THR* 4.2 5.9 - - - +
42F GLU* 3.1 19.0 + - - +
310F ASN* 5.0 1.2 - - - +
312F LYS* 1.3 78.9 + - - +
314F GLY* 1.3 63.4 + - - +
315F ILE* 2.8 35.7 + - + +
316F THR* 3.3 3.3 + - - -
317F ALA* 3.1 23.0 + - - +
336F LEU* 5.9 1.3 - - - -
345F LEU* 3.8 18.9 - - - +
346F THR* 5.3 6.5 - - - +
349F LEU* 3.3 27.9 - - + +
350F THR* 4.6 0.9 - - + -
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Residues in contact with GLY 314 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313F THR* 1.3 74.9 - - - +
315F ILE* 1.3 57.8 + - - +
317F ALA* 3.6 13.8 - - - +
318F ALA* 3.0 27.4 + - - +
321F ARG* 4.7 1.0 + - - -
345F LEU 5.3 3.6 + - - -
346F THR* 5.4 3.8 + - - +
350F THR* 3.5 29.6 + - - +
353F GLU* 3.8 12.7 - - - +
371F ILE* 4.6 1.6 - - - +
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Residues in contact with ILE 315 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28F ILE* 4.1 29.6 - - + -
40F LEU* 4.2 6.3 - - + -
41F GLY* 3.5 44.4 - - - +
42F GLU* 3.7 11.7 - - + +
107F MET* 4.1 6.4 - - - +
313F THR* 2.8 24.1 - - + +
314F GLY* 1.3 77.6 - - - +
316F THR* 1.3 61.5 + - - +
318F ALA* 3.2 14.7 + - - +
319F ALA 3.3 7.8 + - - -
349F LEU* 4.3 5.8 - - + -
350F THR* 4.3 12.1 - - + -
369F LEU* 4.9 0.3 - - - +
371F ILE* 3.7 25.6 - - + +
373F LEU* 4.7 7.0 - - + -
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Residues in contact with THR 316 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42F GLU* 2.5 33.0 + - - +
107F MET* 4.1 9.7 - - - +
282F ASP* 4.8 0.4 - - - +
283F TYR* 3.7 28.9 - - + -
284F ASN* 2.9 29.9 + - - +
310F ASN* 3.5 20.6 - - - +
312F LYS* 4.0 5.4 - - + -
313F THR 3.3 3.8 + - - -
315F ILE* 1.3 71.5 - - - +
317F ALA* 1.3 59.5 + - - +
319F ALA* 3.0 3.2 + - - +
320F ALA* 2.9 25.8 + - - +
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Residues in contact with ALA 317 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310F ASN* 4.4 8.2 + - - +
313F THR 3.1 8.8 + - - +
314F GLY* 3.6 20.9 - - - +
315F ILE 3.2 0.6 - - - -
316F THR* 1.3 74.3 - - - +
318F ALA* 1.3 61.4 + - - +
320F ALA* 3.2 9.3 + - - +
321F ARG* 3.0 34.4 + - - +
335F TYR* 3.7 25.1 - - + +
336F LEU 4.9 6.5 - - - +
353F GLU* 4.3 3.4 - - - +
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Residues in contact with ALA 318 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314F GLY 3.0 9.1 + - - +
315F ILE 3.5 6.1 - - - +
317F ALA* 1.3 74.5 - - - +
319F ALA* 1.3 64.3 + - - +
321F ARG* 3.3 30.0 + - - +
322F HIS* 3.3 21.8 + - - -
369F LEU* 3.5 17.9 - - + +
371F ILE* 3.4 34.1 - - + -
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Residues in contact with ALA 319 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107F MET* 4.0 34.8 - - + -
125F MET* 4.8 1.7 - - - +
283F TYR* 4.3 17.3 - - + -
289F VAL* 4.7 8.5 - - + +
315F ILE 3.3 2.4 + - - -
316F THR* 3.0 10.4 + - - +
318F ALA* 1.3 80.6 - - - +
320F ALA* 1.3 56.6 + - - +
322F HIS* 3.4 1.4 + - - +
323F PHE* 2.9 31.4 + - - +
369F LEU* 3.9 14.3 - - + +
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Residues in contact with ALA 320 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133F LEU* 4.3 4.5 - - - +
283F TYR* 3.5 26.9 + - + +
310F ASN* 3.4 29.6 - - - +
316F THR 2.9 8.5 + - - +
317F ALA* 3.2 8.9 + - - +
319F ALA* 1.3 77.2 - - - +
321F ARG* 1.3 57.2 + - - +
324F GLY* 2.8 28.8 + - - +
333F VAL* 4.5 4.3 - - + +
334F GLU 4.6 3.1 - - - +
335F TYR* 4.5 8.1 - - + -
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Residues in contact with ARG 321 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133F LEU* 3.7 8.8 - - + +
314F GLY 4.8 0.4 + - - -
317F ALA* 3.0 27.8 + - - +
318F ALA* 3.6 29.7 - - - +
319F ALA 3.3 0.4 - - - -
320F ALA* 1.3 77.1 - - - +
322F HIS* 1.3 65.5 + - + +
324F GLY 4.0 0.3 - - - -
325F ILE* 3.2 16.1 + - - +
335F TYR* 2.9 24.0 + - + +
353F GLU* 3.2 23.8 + - - -
354F PRO* 3.6 24.3 - - - +
361F ILE* 3.0 35.4 - - + -
362F GLU 4.0 6.6 + - - -
363F VAL* 3.3 31.4 - - + +
364F SER 6.0 0.2 - - - +
369F LEU 4.4 3.6 + - - -
370F GLY 4.1 14.8 + - - -
371F ILE* 5.5 0.6 - - - +
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Residues in contact with HIS 322 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120F PRO* 3.8 14.4 - - + -
121F ALA* 3.5 9.8 + - + -
122F TYR* 3.0 31.3 + + - +
125F MET* 3.7 23.6 - - + -
318F ALA 3.3 23.3 + - - +
319F ALA 4.0 0.4 - - - +
321F ARG* 1.3 79.1 + - + +
323F PHE* 1.3 65.8 + - - +
325F ILE* 3.1 21.7 + - - +
326F VAL* 3.5 8.7 + - - +
363F VAL* 4.0 11.5 - - + +
364F SER 3.9 11.5 + - - -
366F LYS 4.6 1.1 + - - -
368F GLY 3.3 19.0 + - - -
369F LEU* 3.1 31.6 + - + -
370F GLY* 4.9 1.2 - - - -
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Residues in contact with PHE 323 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125F MET* 3.7 12.2 - - + -
283F TYR* 3.8 28.7 - + + -
289F VAL* 4.5 15.5 - - + -
292F LEU* 3.9 24.2 - - + -
293F LEU* 3.9 28.3 - - + -
296F MET* 4.4 7.0 - - - -
306F LEU* 3.6 28.9 - - + -
308F PRO* 3.9 15.0 - - + -
319F ALA 2.9 18.1 + - - +
322F HIS* 1.3 76.0 - - - +
324F GLY* 1.3 62.1 + - - +
326F VAL* 2.8 22.3 + - + +
327F CYS* 2.9 37.4 + - + +
333F VAL* 5.4 0.4 - - + -
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Residues in contact with GLY 324 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F LYS* 3.6 19.4 + - - +
133F LEU* 3.8 20.4 - - - +
283F TYR* 4.8 0.2 + - - -
320F ALA 2.8 24.2 + - - -
323F PHE* 1.3 75.0 - - - +
325F ILE* 1.3 59.1 + - - +
326F VAL 3.3 0.7 + - - -
327F CYS* 3.6 10.3 + - - +
333F VAL* 4.3 18.9 - - - +
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Residues in contact with ILE 325 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F TYR* 3.5 31.0 - - + -
128F ALA* 4.1 11.9 - - + -
129F GLN 2.9 23.2 + - - -
130F LYS* 3.5 27.8 + - + +
131F ALA 4.7 2.0 - - - +
132F GLN* 3.8 8.3 - - - +
133F LEU* 3.4 35.9 - - + +
321F ARG 3.2 14.6 + - - +
322F HIS* 3.1 19.3 + - - +
323F PHE 3.1 1.2 - - - -
324F GLY* 1.3 76.9 - - - +
326F VAL* 1.3 59.8 + - + +
363F VAL* 3.9 16.8 - - + +
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Residues in contact with VAL 326 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122F TYR* 3.5 25.4 - - + +
125F MET* 3.4 28.7 - - + +
126F GLY* 5.3 0.7 - - - -
127F GLY 3.4 26.0 - - - +
129F GLN* 3.5 22.1 - - - +
293F LEU* 4.4 16.2 - - + -
296F MET* 4.2 11.5 - - + +
322F HIS 3.7 11.9 - - - +
323F PHE* 2.8 10.7 + - + +
325F ILE* 1.3 79.3 - - - +
327F CYS* 1.3 60.9 + - - +
328F HIS* 3.0 11.2 + - - -
79H ARG* 5.3 1.1 - - - -
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Residues in contact with CYS 327 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F LYS* 3.0 19.8 + - - -
296F MET* 3.8 15.9 - - - -
306F LEU* 4.0 9.9 - - - -
323F PHE* 2.9 45.0 + - + +
324F GLY* 3.6 7.8 + - - +
325F ILE 3.6 0.8 - - - -
326F VAL* 1.3 73.3 - - - +
328F HIS* 1.3 61.6 + - - +
329F ILE* 3.2 15.3 - - - -
330F SER* 3.2 36.1 + - - +
333F VAL* 5.2 1.6 - - + -
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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