Contacts of the helix formed by residues 318 - 334 (chain C) in PDB entry 3MQ6
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 318 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60C ASN 3.4 13.2 + - - -
61C GLY* 3.3 20.1 - - - +
62C MET 3.2 21.5 - - - +
63C ASP* 4.5 0.9 - - - +
64C TYR* 3.8 8.5 - - - -
316C PRO* 3.4 3.8 - - - +
317C PRO* 1.3 87.6 - - + +
319C ALA* 1.3 64.7 + - - +
320C ALA* 3.5 4.0 + - - +
321C ASP* 3.1 28.8 + - - +
322C LEU* 3.2 11.8 + - - +
324C ARG* 4.4 3.8 + - - -
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Residues in contact with ALA 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C PRO* 3.4 36.6 - - + +
53C GLY* 3.4 14.1 - - - +
59C ILE 4.8 2.2 + - - +
60C ASN* 3.7 6.1 + - - +
62C MET 4.5 2.2 + - - -
64C TYR* 3.7 23.5 - - + -
67C VAL* 5.7 0.7 - - + -
109C VAL* 4.3 6.4 - - + +
318C THR* 1.3 72.1 - - - +
320C ALA* 1.3 62.3 + - - +
322C LEU* 3.1 10.2 + - - +
323C ALA* 3.0 21.7 + - - +
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Residues in contact with ALA 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLY* 4.3 0.9 - - - -
60C ASN* 3.1 29.9 + - + +
61C GLY* 5.2 1.3 - - - -
132C TYR* 3.4 23.4 - - + +
318C THR* 3.1 3.7 - - - +
319C ALA* 1.3 77.8 - - - +
321C ASP* 1.3 58.6 + - - +
323C ALA* 3.3 2.3 + - - +
324C ARG* 2.8 51.0 + - - +
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Residues in contact with ASP 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C TYR* 2.5 28.6 + - - -
317C PRO* 3.2 26.6 - - + +
318C THR* 3.1 22.8 + - - +
320C ALA* 1.3 80.5 - - - +
322C LEU* 1.3 55.9 + - - +
324C ARG* 3.6 25.9 + - - +
325C ARG* 2.8 31.5 + - - +
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Residues in contact with LEU 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64C TYR* 3.9 18.2 - - + +
106C SER* 3.9 37.9 - - - +
109C VAL* 4.1 14.4 - - + -
110C MET* 4.8 13.5 - - + -
278C HIS* 3.7 31.4 - - + +
314C TYR* 3.3 20.3 + - + +
316C PRO* 4.3 6.5 - - + -
318C THR 3.2 8.2 + - - +
319C ALA* 3.1 10.2 + - - +
321C ASP* 1.3 79.3 - - - +
323C ALA* 1.3 62.3 + - - +
325C ARG* 3.5 3.4 + - + +
326C PHE* 3.1 22.8 + - + +
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Residues in contact with ALA 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C GLY* 5.1 0.4 - - - +
54C PHE* 4.5 4.0 - - + -
109C VAL* 4.3 8.7 - - + +
113C CYS* 3.6 25.3 - - - -
132C TYR* 3.4 32.8 - - + +
319C ALA 3.0 10.6 + - - +
320C ALA 3.5 2.5 - - - +
322C LEU* 1.3 78.4 - - - +
324C ARG* 1.3 60.1 + - - +
326C PHE* 3.2 2.3 + - - +
327C PHE* 3.0 33.3 + - + -
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Residues in contact with ARG 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132C TYR* 3.6 22.6 - - + +
133C SER* 5.9 4.3 - - - +
318C THR* 4.4 4.6 + - - -
320C ALA* 2.8 34.7 + - - +
321C ASP* 3.6 37.2 + - - +
323C ALA* 1.3 70.3 - - - +
325C ARG* 1.3 66.0 + - - +
327C PHE* 3.5 7.7 + - - +
328C ALA* 3.1 23.9 + - - +
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Residues in contact with ARG 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237C LEU* 5.8 0.2 - - - +
276C GLU* 2.5 47.1 + - - -
278C HIS* 3.6 8.7 + - - -
311C ARG* 3.3 10.8 - - - +
312C GLU* 2.9 36.4 + - - +
314C TYR* 3.4 44.9 - - + +
321C ASP* 2.8 22.4 + - - +
322C LEU* 3.8 5.1 - - + +
324C ARG* 1.3 73.0 - - - +
326C PHE* 1.3 58.4 + - - +
328C ALA* 3.3 7.0 + - - +
329C PHE* 3.0 30.4 + - + +
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Residues in contact with PHE 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110C MET* 3.6 62.1 - - + -
113C CYS* 3.4 26.0 - - + -
114C ALA 4.3 1.8 - - - -
145C VAL* 5.0 0.4 - - + -
147C VAL* 3.8 10.1 - - + -
191C VAL* 3.7 26.0 - - + -
237C LEU* 4.5 5.6 - - + -
322C LEU* 3.1 19.5 + - + +
323C ALA 3.8 3.4 - - - +
324C ARG 3.2 0.4 - - - -
325C ARG* 1.3 75.8 - - - +
327C PHE* 1.3 65.7 + - - +
329C PHE* 3.2 17.0 + + + +
330C LEU* 3.0 51.3 + - + +
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Residues in contact with PHE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54C PHE* 4.2 6.7 - + - -
113C CYS* 3.3 52.3 - - + -
116C ARG* 4.2 11.2 - - + -
117C TRP* 4.5 16.3 - + + -
126C TRP* 3.8 29.6 - + + -
132C TYR* 3.8 40.4 - + + -
133C SER 5.2 6.7 - - - +
135C PRO* 5.3 4.6 - - + +
323C ALA* 3.0 30.0 + - + +
324C ARG* 3.8 5.2 - - - +
326C PHE* 1.3 76.0 - - - +
328C ALA* 1.3 57.3 + - - +
330C LEU* 3.2 8.0 + - + +
331C ASN* 3.0 28.5 + - - +
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Residues in contact with ALA 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324C ARG 3.1 18.3 + - - +
325C ARG* 3.6 7.2 - - - +
326C PHE 3.2 0.2 - - - -
327C PHE* 1.3 72.9 - - - +
329C PHE* 1.3 67.3 + - - +
331C ASN* 3.4 8.6 + - - +
332C GLU* 3.2 22.2 + - - +
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Residues in contact with PHE 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191C VAL* 5.8 0.4 - - + -
236C SER* 3.5 24.5 - - - -
237C LEU* 3.8 36.8 - - + -
274C GLU* 4.5 7.0 - - + -
276C GLU* 5.4 0.2 - - - -
311C ARG* 3.6 40.8 - - - +
325C ARG* 3.0 17.5 + - + +
326C PHE* 3.4 14.8 - + + +
328C ALA* 1.3 77.3 - - - +
330C LEU* 1.3 68.6 + - + +
332C GLU* 3.3 6.9 + - + +
333C ARG* 2.7 68.2 + - + +
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Residues in contact with LEU 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113C CYS 5.2 0.2 - - - +
114C ALA* 5.1 1.6 - - - -
117C TRP* 3.7 44.1 - - + -
145C VAL* 4.0 32.8 - - + -
191C VAL* 4.5 3.8 - - + -
236C SER* 6.0 0.7 - - - -
326C PHE* 3.0 53.7 + - + +
327C PHE* 3.2 10.7 + - + +
329C PHE* 1.3 86.2 - - + +
331C ASN* 1.3 61.1 + - - +
333C ARG* 4.4 0.4 - - - +
334C MET* 2.8 44.2 + - + +
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Residues in contact with ASN 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C TRP* 3.8 10.6 - - + -
135C PRO* 3.4 12.9 - - + +
136C THR* 2.8 47.2 + - - +
137C LEU* 3.1 29.8 + - - +
327C PHE 3.0 13.2 + - - +
328C ALA* 3.5 12.6 - - - +
329C PHE 3.3 0.2 - - - -
330C LEU* 1.3 78.3 - - - +
332C GLU* 1.3 60.7 + - - +
335C GLU* 4.4 4.2 - - - +
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Residues in contact with GLU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311C ARG* 5.5 5.7 + - - -
328C ALA 3.2 12.0 + - - +
329C PHE* 3.9 6.5 - - + +
330C LEU 3.2 0.4 - - - -
331C ASN* 1.3 79.2 - - - +
333C ARG* 1.3 71.5 + - + +
335C GLU* 3.0 23.4 - - - +
336C LEU* 4.9 2.4 - - - +
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Residues in contact with ARG 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C GLY 4.0 16.0 + - - -
235C ILE 3.7 7.9 + - - -
236C SER* 3.5 41.5 + - - +
271C PRO* 5.0 12.3 - - - +
272C LYS* 3.4 16.0 + - - +
273C VAL* 5.8 0.2 - - - +
274C GLU* 3.3 28.3 + - - +
329C PHE* 2.7 57.5 + - + +
330C LEU* 4.3 1.6 - - - +
332C GLU* 1.3 77.4 - - + +
334C MET* 1.3 62.5 + - - +
335C GLU 3.1 4.7 + - - -
336C LEU* 3.1 47.1 + - - +
337C VAL* 4.6 0.9 + - - +
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Residues in contact with MET 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117C TRP* 3.8 18.2 - - + -
137C LEU* 3.5 14.8 - - + -
143C ARG* 3.2 51.5 + - + +
145C VAL* 3.7 17.0 - - + -
193C VAL* 3.8 14.1 - - + -
236C SER* 4.3 14.8 - - - -
330C LEU* 2.8 37.4 + - + +
333C ARG* 1.3 76.6 - - - +
335C GLU* 1.3 63.3 + - - +
336C LEU 3.0 1.8 - - - -
337C VAL* 3.2 38.9 + - + +
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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
------------------------------------------------------------
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