Contacts of the helix formed by residues 313 - 327 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B THR* 4.2 2.0 - - - +
42B GLU* 3.0 25.3 + - - +
310B ASN* 5.1 1.4 - - - +
312B LYS* 1.3 82.0 - - - +
314B GLY* 1.3 66.6 + - - +
315B ILE* 2.9 28.1 + - + +
316B THR* 3.2 3.1 + - - -
317B ALA* 3.0 19.9 + - - +
336B LEU* 6.2 0.7 - - - -
345B LEU* 3.7 26.2 - - - +
346B THR* 5.5 3.1 - - - +
349B LEU* 3.6 28.3 - - + +
350B THR* 4.8 0.4 - - + -
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Residues in contact with GLY 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B THR* 1.3 75.1 - - - +
315B ILE* 1.3 60.4 + - - +
317B ALA* 3.7 10.4 - - - +
318B ALA* 3.1 23.4 + - - +
321B ARG* 4.7 0.7 + - - -
345B LEU 5.2 4.8 + - - -
346B THR* 5.5 4.2 + - - +
349B LEU* 5.5 0.2 - - - +
350B THR* 3.5 32.3 + - - +
353B GLU* 3.8 12.8 - - - +
371B ILE* 4.6 1.0 - - - +
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Residues in contact with ILE 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.8 36.1 - - + -
40B LEU* 4.9 5.4 - - + -
41B GLY* 3.5 42.2 - - - +
42B GLU* 3.8 9.9 - - - +
107B MET* 3.8 5.1 - - - +
313B THR* 2.9 22.7 - - + +
314B GLY* 1.3 77.1 - - - +
316B THR* 1.3 64.2 + - - +
318B ALA* 3.1 14.9 + - - +
319B ALA* 3.2 10.9 + - - +
349B LEU* 4.4 3.8 - - + -
350B THR* 4.5 9.9 - - + -
369B LEU* 4.9 0.3 - - - +
371B ILE* 3.9 29.8 - - + +
373B LEU* 4.6 7.6 - - + -
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Residues in contact with THR 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 2.6 33.2 + - - +
107B MET* 4.1 6.6 - - - +
283B TYR* 3.7 27.1 - - + -
284B ASN* 3.1 27.5 + - - +
310B ASN* 3.3 22.2 - - - +
312B LYS* 4.0 5.4 - - + -
313B THR 3.2 3.8 + - - -
315B ILE* 1.3 74.6 - - - +
317B ALA* 1.3 58.3 + - - +
319B ALA* 2.9 8.6 + - - +
320B ALA* 2.8 26.9 + - - +
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310B ASN* 4.3 9.1 + - - +
313B THR 3.0 16.2 + - - +
314B GLY* 3.7 12.6 - - - +
315B ILE 3.2 0.2 - - - -
316B THR* 1.3 76.2 - - - +
318B ALA* 1.3 57.4 + - - +
320B ALA* 3.3 8.4 + - - +
321B ARG* 2.9 38.3 + - - +
335B TYR* 3.8 25.8 - - + +
336B LEU* 4.7 8.1 - - + +
353B GLU* 4.4 3.8 - - - +
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Residues in contact with ALA 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314B GLY 3.1 8.5 + - - +
315B ILE 3.1 4.0 + - - +
317B ALA* 1.3 74.7 - - - +
319B ALA* 1.3 64.6 + - - +
321B ARG* 3.3 33.8 + - - +
322B HIS* 3.2 26.4 - - - -
369B LEU* 3.5 20.6 - - + +
371B ILE* 3.5 25.1 - - + -
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B MET* 3.9 37.7 - - + -
125B MET* 4.7 2.5 - - - +
283B TYR* 4.3 13.0 - - + -
289B VAL* 4.8 8.5 - - + +
315B ILE 3.2 4.4 + - - +
316B THR* 2.9 9.9 + - - +
318B ALA* 1.3 77.7 - - - +
320B ALA* 1.3 57.0 + - - +
322B HIS* 3.5 1.6 + - - +
323B PHE* 3.0 31.4 + - - +
369B LEU* 4.0 14.5 - - + +
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 4.3 4.4 - - - +
283B TYR* 3.4 30.0 + - + +
310B ASN* 3.4 27.6 - - - +
316B THR 2.8 11.7 + - - +
317B ALA 3.7 4.7 - - - +
319B ALA* 1.3 75.0 - - - +
321B ARG* 1.3 59.4 + - - +
324B GLY* 2.7 29.1 + - - -
333B VAL* 4.6 5.4 - - + +
334B GLU 4.6 3.6 - - - +
335B TYR* 4.7 6.1 - - + -
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Residues in contact with ARG 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B LEU* 3.7 8.9 - - + +
314B GLY 4.7 0.6 + - - -
317B ALA* 2.9 28.7 + - - +
318B ALA* 3.3 31.8 - - - +
319B ALA 3.3 0.4 - - - -
320B ALA* 1.3 76.9 - - - +
322B HIS* 1.3 62.6 + - + +
324B GLY* 3.9 0.5 - - - -
325B ILE 3.2 17.3 + - - -
335B TYR* 2.9 23.3 + - + +
353B GLU* 3.1 25.5 + - - -
354B PRO* 3.6 19.4 - - - +
361B ILE* 3.1 34.3 - - + -
362B GLU 3.7 11.6 + - - -
363B VAL* 3.4 30.3 - - + +
364B SER 5.7 1.4 - - - +
369B LEU 4.5 2.8 + - - -
370B GLY 4.4 12.9 + - - -
371B ILE* 5.3 2.0 - - - +
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Residues in contact with HIS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PRO* 3.8 7.6 - - + -
121B ALA* 3.6 8.9 + - + -
122B TYR* 3.0 43.5 + + - +
125B MET* 3.8 21.1 - - + -
318B ALA 3.2 25.5 + - - +
319B ALA 4.1 0.7 - - - +
321B ARG* 1.3 76.7 + - + +
323B PHE* 1.3 65.3 + - - +
325B ILE* 3.4 9.4 - - - +
326B VAL* 3.2 22.0 - - - +
363B VAL* 4.2 10.6 - - + +
364B SER* 3.9 11.7 + - - -
366B LYS 4.5 0.9 - - - -
368B GLY 3.3 17.3 - - - -
369B LEU* 3.1 33.7 + - + -
370B GLY* 4.2 1.6 + - - -
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Residues in contact with PHE 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B MET* 3.7 16.3 - - + -
283B TYR* 3.9 27.1 - + + -
289B VAL* 4.6 8.3 - - + -
292B LEU* 3.7 27.1 - - + -
293B LEU* 3.8 28.9 - - + -
296B MET* 4.4 4.7 - - - -
306B LEU* 3.5 28.7 - - + -
308B PRO* 4.0 13.5 - - + -
319B ALA 3.0 18.0 + - - +
320B ALA 4.3 0.2 - - - +
322B HIS* 1.3 76.8 - - - +
324B GLY* 1.3 60.0 + - - +
326B VAL* 3.1 5.6 + - + +
327B CYS* 2.9 54.3 + - + +
333B VAL* 5.2 1.3 - - + -
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Residues in contact with GLY 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B LYS* 3.5 20.8 + - - +
133B LEU* 3.9 21.2 - - - +
320B ALA 2.7 21.0 + - - -
323B PHE* 1.3 78.4 - - - +
325B ILE* 1.3 59.4 + - - +
326B VAL 3.1 1.0 + - - -
327B CYS* 3.5 8.6 + - - +
333B VAL* 4.4 18.1 - - - +
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Residues in contact with ILE 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B TYR* 3.5 32.5 - - + -
128B ALA* 3.9 14.6 - - + -
129B GLN* 2.7 30.0 + - - -
130B LYS* 3.3 46.1 + - + +
131B ALA 4.5 2.5 - - - +
132B GLN* 3.7 22.7 - - - +
133B LEU* 3.7 9.4 - - + +
321B ARG 3.2 14.9 + - - +
322B HIS* 3.4 15.0 - - - +
324B GLY* 1.3 74.7 - - - +
326B VAL* 1.3 52.0 + - - +
363B VAL* 4.3 13.9 - - + -
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B TYR* 3.5 31.6 - - + +
125B MET* 3.4 28.7 - - + +
126B GLY* 5.3 0.7 - - - -
127B GLY 3.8 16.6 - - - +
129B GLN* 3.8 18.0 - - - +
293B LEU* 4.3 16.2 - - + -
296B MET* 4.3 10.4 - - + +
322B HIS 3.2 15.5 - - - +
323B PHE* 3.1 11.9 + - + +
325B ILE* 1.3 81.7 - - - +
327B CYS* 1.3 58.2 + - - +
328B HIS* 2.9 13.7 + - - -
79D ARG* 5.4 0.9 - - - -
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Residues in contact with CYS 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LYS* 3.0 19.1 + - - -
296B MET* 3.8 18.2 - - - -
306B LEU* 4.0 10.3 - - - -
323B PHE* 2.9 42.3 + - + +
324B GLY* 3.5 7.7 + - - +
326B VAL* 1.3 75.5 - - - +
328B HIS* 1.3 60.5 + - - +
329B ILE* 3.1 18.4 + - - -
330B SER* 3.2 31.1 + - - +
333B VAL* 5.3 2.9 - - + -
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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