Contacts of the helix formed by residues 313 - 327 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C THR* 4.1 6.6 - - - +
42C GLU* 3.0 21.7 + - - +
310C ASN* 5.1 1.0 - - - +
312C LYS* 1.3 83.1 + - - +
314C GLY* 1.3 68.2 + - - +
315C ILE* 2.9 21.8 + - + +
316C THR* 3.2 2.6 + - - -
317C ALA* 3.0 21.3 + - - +
345C LEU* 3.8 22.8 - - - +
346C THR* 5.5 2.0 - - - -
349C LEU* 3.1 38.4 - - + +
350C THR* 4.8 0.4 - - + -
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Residues in contact with GLY 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313C THR* 1.3 78.0 - - - +
315C ILE* 1.3 59.5 + - - +
317C ALA* 3.6 9.7 - - - +
318C ALA* 3.0 23.6 + - - +
321C ARG* 4.8 0.9 + - - -
345C LEU 5.1 4.4 + - - -
346C THR* 5.4 4.6 + - - +
350C THR* 3.5 32.2 + - - +
353C GLU* 3.8 12.8 - - - +
371C ILE* 4.7 1.0 - - - +
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Residues in contact with ILE 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ILE* 3.7 33.9 - - + -
40C LEU* 4.3 5.2 - - + +
41C GLY* 3.5 40.6 - - - +
42C GLU* 3.7 14.6 - - + +
107C MET* 3.8 5.5 - - - +
313C THR* 2.9 23.0 - - + +
314C GLY* 1.3 79.2 - - - +
316C THR* 1.3 62.9 + - - +
318C ALA* 3.2 10.6 + - - +
319C ALA* 3.3 10.7 + - - +
349C LEU* 3.8 8.5 - - + -
350C THR* 4.2 3.3 - - + +
369C LEU* 4.5 0.3 - - - +
371C ILE* 4.0 33.6 - - + +
373C LEU* 4.6 7.4 - - + -
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Residues in contact with THR 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C GLU* 2.5 29.9 + - - +
107C MET* 3.9 11.7 - - - +
283C TYR* 3.5 39.5 - - + -
284C ASN* 3.1 23.3 + - - +
310C ASN* 3.5 15.9 - - - +
312C LYS* 4.1 4.7 - - + -
313C THR 3.2 3.3 + - - -
315C ILE* 1.3 75.3 - - - +
317C ALA* 1.3 60.4 + - - +
319C ALA* 2.9 3.7 + - - +
320C ALA* 2.8 26.2 + - - +
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Residues in contact with ALA 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C ASN* 4.2 9.7 + - - +
313C THR 3.0 14.7 + - - +
314C GLY* 3.6 14.6 - - - +
315C ILE 3.3 0.2 - - - -
316C THR* 1.3 75.4 - - - +
318C ALA* 1.3 57.1 + - - +
320C ALA* 3.2 9.6 + - - +
321C ARG* 2.9 38.2 + - - +
335C TYR* 3.7 26.7 - - + +
336C LEU* 4.9 7.0 - - + +
353C GLU* 4.3 3.1 - - - +
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Residues in contact with ALA 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C GLY 3.0 10.1 + - - +
315C ILE 3.5 4.5 - - - +
316C THR 3.2 0.2 - - - -
317C ALA* 1.3 74.2 - - - +
319C ALA* 1.3 62.0 + - - +
321C ARG* 3.4 30.4 + - - +
322C HIS* 3.2 31.3 + - - -
369C LEU* 3.6 11.9 - - + +
371C ILE* 3.5 32.8 - - + -
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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
----------------------------------------------------------
107C MET* 4.0 33.7 - - + -
125C MET* 4.4 2.9 - - - +
283C TYR* 4.4 15.3 - - + -
289C VAL* 4.8 8.9 - - + +
315C ILE 3.3 3.2 + - - +
316C THR* 2.9 10.6 + - - +
318C ALA* 1.3 79.8 - - - +
320C ALA* 1.3 50.4 + - - +
322C HIS* 3.3 2.4 + - - +
323C PHE* 2.8 36.9 + - - +
369C LEU* 4.0 15.4 - - + +
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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
----------------------------------------------------------
133C LEU* 4.0 4.2 - - - +
283C TYR* 3.4 31.3 + - + +
310C ASN* 3.5 27.8 - - - +
316C THR 2.8 11.7 + - - +
317C ALA 3.5 7.4 - - - +
319C ALA* 1.3 69.5 - - - +
321C ARG* 1.3 58.7 + - - +
324C GLY* 2.7 31.7 + - - -
333C VAL* 4.5 4.9 - - + +
334C GLU 4.6 3.1 - - - +
335C TYR* 4.8 5.8 - - + -
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Residues in contact with ARG 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133C LEU* 3.5 9.2 - - - +
314C GLY 4.8 0.8 + - - -
317C ALA* 2.9 17.6 + - - +
318C ALA* 3.4 41.6 + - - +
319C ALA 3.3 0.4 - - - -
320C ALA* 1.3 78.3 - - - +
322C HIS* 1.3 63.8 + - + +
325C ILE* 3.2 15.6 + - - +
335C TYR* 2.8 35.1 + - + -
352C ASN 5.7 0.4 + - - -
353C GLU* 3.1 23.2 + - - -
354C PRO* 3.6 23.0 - - - +
361C ILE* 3.0 32.3 - - + -
362C GLU 4.0 4.6 + - - -
363C VAL* 3.3 29.7 - - + +
364C SER 5.7 1.6 - - - +
369C LEU 4.6 2.2 + - - -
370C GLY 4.2 13.7 + - - -
371C ILE* 5.5 0.8 - - - +
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Residues in contact with HIS 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C PRO* 3.6 21.3 - - + -
121C ALA* 3.6 3.8 - - + -
122C TYR* 3.0 31.5 + + - +
125C MET* 3.7 22.2 - - + -
318C ALA 3.2 22.1 + - - +
319C ALA 3.9 4.9 - - - +
321C ARG* 1.3 79.7 - - + +
323C PHE* 1.3 65.7 + - - +
324C GLY 3.4 0.2 + - - -
325C ILE* 3.4 18.0 + - - +
326C VAL* 3.6 10.2 + - - +
363C VAL* 4.0 8.9 - - + +
364C SER* 3.7 14.6 + - - -
366C LYS 4.7 1.2 + - - -
368C GLY 3.5 17.2 + - - -
369C LEU* 3.3 33.2 + - + -
370C GLY* 5.1 0.6 - - - -
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Residues in contact with PHE 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125C MET* 3.7 11.1 - - + -
283C TYR* 3.9 31.0 - + + -
289C VAL* 4.4 14.1 - - + -
292C LEU* 4.0 20.2 - - + -
293C LEU* 3.7 31.2 - - + -
296C MET* 4.4 7.2 - - + -
306C LEU* 3.8 22.0 - - + -
308C PRO* 4.0 19.7 - - + -
319C ALA 2.8 21.2 + - - +
320C ALA 4.2 0.2 - - - +
322C HIS* 1.3 72.5 - - - +
324C GLY* 1.3 65.3 + - - +
326C VAL* 3.0 7.7 + - + +
327C CYS* 3.0 47.1 + - + +
333C VAL* 5.4 1.3 - - + -
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Residues in contact with GLY 324 (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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130C LYS* 3.6 19.9 + - - +
133C LEU* 3.6 20.7 - - - +
320C ALA 2.7 24.2 + - - -
321C ARG 3.8 0.2 - - - -
323C PHE* 1.3 74.6 - - - +
325C ILE* 1.3 59.6 + - - +
326C VAL 3.3 0.7 + - - -
327C CYS* 3.3 10.7 + - - +
333C VAL* 4.4 17.5 - - - +
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Residues in contact with ILE 325 (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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122C TYR* 3.6 31.0 - - + -
128C ALA* 3.9 15.0 - - + -
129C GLN 2.7 30.9 + - - -
130C LYS* 3.4 34.9 + - + +
131C ALA 4.3 2.7 - - - +
132C GLN* 3.7 8.3 - - - +
133C LEU* 3.6 32.0 - - + +
321C ARG 3.2 13.4 + - - +
322C HIS 3.4 12.6 - - - +
323C PHE 3.2 0.4 - - - -
324C GLY* 1.3 75.7 - - - +
326C VAL* 1.3 54.2 + - - +
363C VAL* 4.1 15.7 - - + -
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Residues in contact with VAL 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A ARG* 5.2 1.1 - - - -
122C TYR* 3.7 22.4 - - + +
125C MET* 3.5 27.1 - - + +
127C GLY 3.3 25.4 - - - +
129C GLN* 3.9 13.7 - - - +
293C LEU* 4.3 15.9 - - + -
296C MET* 4.2 12.4 - - + +
322C HIS 3.6 13.5 - - - +
323C PHE* 3.0 12.0 + - + +
325C ILE* 1.3 81.5 - - - +
327C CYS* 1.3 58.7 + - - +
328C HIS* 2.8 19.9 + - - -
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Residues in contact with CYS 327 (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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130C LYS* 3.1 14.5 + - - -
296C MET* 3.9 16.6 - - - -
306C LEU* 4.0 12.3 - - - -
323C PHE* 3.0 43.8 + - + +
324C GLY* 3.3 9.4 + - - +
326C VAL* 1.3 73.9 - - - +
328C HIS* 1.3 56.0 + - - +
329C ILE* 2.9 25.7 + - - -
330C SER* 3.0 33.2 + - - +
333C VAL* 5.2 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