Contacts of the helix formed by residues 313 - 325 (chain X) 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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26X THR* 4.1 2.8 - - - +
42X GLU* 3.1 21.9 + - - +
310X ASN* 5.0 1.0 - - - +
312X LYS* 1.3 83.3 + - - +
314X GLY* 1.3 76.1 + - - +
315X ILE* 3.1 17.2 + - + +
316X THR* 3.2 3.8 + - - -
317X ALA* 3.1 19.3 + - - +
336X LEU* 6.3 0.2 - - - -
345X LEU* 3.7 29.8 - - - +
346X THR* 5.3 1.8 - - - -
349X LEU* 2.9 42.3 - - + +
350X THR* 4.7 0.7 - - + -
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Residues in contact with GLY 314 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313X THR* 1.3 78.2 - - - +
315X ILE* 1.3 62.3 + - - +
317X ALA* 3.6 11.0 - - - +
318X ALA* 3.1 21.8 + - - +
321X ARG* 4.8 0.9 + - - -
345X LEU 5.0 4.4 + - - -
346X THR* 5.3 4.2 + - - +
350X THR* 3.8 16.8 + - - +
353X GLU* 3.8 23.9 - - - +
371X ILE* 4.7 1.2 - - - +
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Residues in contact with ILE 315 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28X ILE* 4.0 32.3 - - + -
40X LEU* 4.1 4.7 - - + +
41X GLY* 3.7 34.8 - - - +
42X GLU* 3.8 16.6 - - + +
107X MET* 4.0 5.1 - - - +
313X THR* 3.1 6.8 - - + +
314X GLY* 1.3 76.7 - - - +
316X THR* 1.3 61.6 + - - +
318X ALA* 3.3 13.7 + - - +
319X ALA* 3.3 11.4 + - - +
349X LEU* 3.9 21.8 - - + -
350X THR* 4.1 4.0 - - + +
369X LEU* 4.6 0.7 - - - +
371X ILE* 4.0 26.6 - - + +
373X LEU* 4.4 14.4 - - + -
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Residues in contact with THR 316 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42X GLU* 2.2 41.0 + - - +
107X MET* 4.1 10.3 - - + +
283X TYR* 3.8 28.7 - - + -
284X ASN* 3.3 20.8 + - - +
310X ASN* 3.5 19.7 - - - +
312X LYS* 3.8 6.5 - - + -
313X THR 3.2 4.7 + - - -
315X ILE* 1.3 72.6 - - - +
317X ALA* 1.3 60.4 + - - +
319X ALA* 3.1 2.3 + - - +
320X ALA* 2.8 26.2 + - - +
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Residues in contact with ALA 317 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310X ASN* 4.4 8.9 + - - +
313X THR 3.1 14.2 + - - +
314X GLY* 3.8 13.0 - - - +
315X ILE 3.3 0.6 - - - -
316X THR* 1.3 76.5 - - - +
318X ALA* 1.3 58.1 + - - +
320X ALA* 3.2 8.8 + - - +
321X ARG* 2.9 38.9 + - - +
335X TYR* 3.6 27.3 - - + +
336X LEU* 4.7 8.1 - - + +
353X GLU* 4.5 2.7 - - - +
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Residues in contact with ALA 318 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314X GLY 3.1 9.7 + - - +
315X ILE 3.5 9.4 - - - +
316X THR 3.2 0.2 - - - -
317X ALA* 1.3 77.0 - - - +
319X ALA* 1.3 62.9 + - - +
321X ARG* 3.2 25.6 + - - +
322X HIS* 3.0 28.9 + - - -
369X LEU* 3.5 27.8 - - + +
371X ILE* 3.6 20.4 - - + +
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Residues in contact with ALA 319 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107X MET* 4.0 39.0 - - + -
125X MET* 4.5 2.6 - - - +
283X TYR* 4.3 11.4 - - + -
289X VAL* 4.8 8.0 - - + +
315X ILE 3.3 2.4 + - - -
316X THR 3.1 8.8 + - - +
318X ALA* 1.3 78.4 - - - +
320X ALA* 1.3 57.5 + - - +
322X HIS* 3.4 1.2 + - - +
323X PHE* 2.8 32.9 + - - +
369X LEU* 3.8 15.5 - - + +
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Residues in contact with ALA 320 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133X LEU* 4.4 3.0 - - - +
283X TYR* 3.4 28.6 + - + +
310X ASN* 3.4 29.6 - - - +
316X THR 2.8 10.1 + - - +
317X ALA* 3.5 7.6 - - - +
319X ALA* 1.3 75.2 - - - +
321X ARG* 1.3 58.3 + - - +
324X GLY* 2.7 32.2 + - - -
333X VAL* 4.4 3.8 - - + +
334X GLU 4.6 2.7 - - - +
335X TYR* 4.5 7.6 - - + -
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Residues in contact with ARG 321 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133X LEU* 3.7 12.2 - - + +
314X GLY 4.8 0.4 + - - -
317X ALA* 2.9 25.1 + - - +
318X ALA* 3.5 31.5 - - - +
320X ALA* 1.3 75.3 - - - +
322X HIS* 1.3 66.0 + - + +
324X GLY* 3.9 0.3 - - - -
325X ILE* 3.3 18.4 + - - +
335X TYR* 2.7 33.5 + - + -
353X GLU* 2.9 25.5 + - - -
354X PRO* 3.5 21.1 - - - +
361X ILE* 2.7 39.3 - - + -
362X GLU 4.0 7.5 + - - -
363X VAL* 3.7 26.2 - - + +
364X SER 5.8 1.2 - - - +
369X LEU 4.6 2.6 + - - -
370X GLY 4.3 12.5 + - - -
371X ILE* 5.5 1.0 - - - +
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Residues in contact with HIS 322 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120X PRO* 3.7 15.7 - - + -
121X ALA* 3.4 12.4 + - + -
122X TYR* 2.9 33.6 + + - +
125X MET* 3.7 23.6 - - + -
318X ALA* 3.0 27.3 + - - +
319X ALA 3.9 0.7 - - - +
321X ARG* 1.3 79.1 + - + +
323X PHE* 1.3 65.6 + - - +
325X ILE* 3.3 17.7 - - - +
326X VAL* 3.4 10.9 - - - +
363X VAL* 4.0 12.6 - - + +
364X SER* 3.9 11.7 + - - -
366X LYS 4.7 1.3 + - - -
368X GLY 3.3 18.4 + - - -
369X LEU* 3.4 28.0 + - + -
370X GLY* 5.1 0.6 - - - -
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Residues in contact with PHE 323 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125X MET* 3.6 11.1 - - + -
283X TYR* 3.8 29.8 - + + -
289X VAL* 4.2 18.8 - - + -
292X LEU* 3.9 22.2 - - + -
293X LEU* 3.7 27.6 - - + -
296X MET* 4.6 5.6 - - - -
306X LEU* 3.7 21.1 - - + -
308X PRO* 3.9 20.0 - - + -
319X ALA 2.8 21.5 + - - +
322X HIS* 1.3 72.0 - - - +
324X GLY* 1.3 65.3 + - - +
326X VAL* 3.0 7.7 + - + +
327X CYS* 3.0 47.8 + - + +
333X VAL* 5.3 1.6 - - + -
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Residues in contact with GLY 324 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130X LYS* 3.2 24.6 + - - +
133X LEU* 3.8 16.6 - - - -
283X TYR* 4.9 0.2 + - - -
320X ALA 2.7 23.9 + - - -
321X ARG 3.9 1.1 - - - -
323X PHE* 1.3 74.1 - - - +
325X ILE* 1.3 59.7 + - - +
326X VAL 3.1 1.1 + - - -
327X CYS* 3.5 7.1 + - - +
333X VAL* 4.2 18.4 - - - -
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Residues in contact with ILE 325 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122X TYR* 3.6 29.8 - - + -
128X ALA* 3.9 14.4 - - + -
129X GLN 2.7 30.2 + - - -
130X LYS* 3.3 38.0 + - + +
131X ALA 4.6 2.2 - - - +
132X GLN* 3.9 6.1 - - - +
133X LEU* 3.9 27.0 - - + +
321X ARG 3.3 12.9 + - - +
322X HIS* 3.3 17.5 - - - +
324X GLY* 1.3 74.8 - - - +
326X VAL* 1.3 52.7 + - + +
363X VAL* 4.0 19.3 - - + -
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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