Contacts of the helix formed by residues 331 - 340 (chain M) in PDB entry 5IIO
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 SER 331 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270M GLN* 4.4 3.8 + - - -
329M SER* 2.7 21.0 + - - -
330M GLU* 1.3 79.2 - - - +
332M VAL* 1.3 64.3 + - - +
333M PRO 3.4 0.7 - - - -
334M VAL* 3.0 7.1 + - - +
335M LEU* 2.9 39.2 + - - +
353M TYR* 3.4 42.0 + - - -
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Residues in contact with VAL 332 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265M LYS* 5.4 1.1 - - + -
266M ALA* 4.1 18.2 - - + +
269M VAL* 3.9 15.3 - - + +
270M GLN* 3.8 36.1 - - + +
328M ILE* 3.6 22.7 - - + -
329M SER 3.2 13.2 + - - +
331M SER* 1.3 76.9 + - - +
333M PRO* 1.3 73.4 - - + +
334M VAL 3.2 0.2 + - - -
335M LEU* 3.2 4.3 + - - +
336M GLU* 2.9 30.4 + - - +
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Residues in contact with PRO 333 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328M ILE* 5.8 0.4 - - + -
329M SER 4.2 1.8 - - - +
330M GLU* 3.5 18.4 - - - +
332M VAL* 1.3 97.3 - - + +
334M VAL* 1.3 57.8 + - + +
336M GLU* 3.7 9.2 - - + +
337M LEU* 3.0 26.7 + - - +
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Residues in contact with VAL 334 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330M GLU 4.9 6.7 - - - +
331M SER 3.0 9.0 + - - +
333M PRO* 1.3 77.7 - - + +
335M LEU* 1.3 60.7 + - - +
337M LEU* 3.1 8.6 + - + +
338M PHE* 2.9 60.7 + - + -
353M TYR* 3.6 22.2 - - + -
358M ARG* 3.8 35.7 - - + +
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Residues in contact with LEU 335 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269M VAL* 4.0 27.0 - - + +
270M GLN* 4.0 21.5 - - + -
331M SER* 2.9 37.6 + - - +
332M VAL* 3.2 4.7 + - - +
334M VAL* 1.3 78.1 - - - +
336M GLU* 1.3 55.0 + - - +
338M PHE* 3.5 0.8 + - + -
339M SER* 2.9 32.0 + - - -
349M ALA* 3.6 39.9 - - + +
350M GLN* 3.9 14.8 - - + +
353M TYR* 3.9 19.1 - - + -
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Residues in contact with GLU 336 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265M LYS* 3.6 40.6 - - - +
269M VAL* 3.8 16.7 - - + +
332M VAL* 2.9 22.5 + - - +
333M PRO* 3.7 9.1 - - + +
335M LEU* 1.3 71.7 - - - +
337M LEU* 1.3 68.1 + - - +
339M SER* 3.4 1.7 + - - -
340M ASN* 2.9 45.4 + - - +
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Residues in contact with LEU 337 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333M PRO 3.0 14.6 + - - +
334M VAL* 3.2 10.8 - - + +
336M GLU* 1.3 78.5 - - - +
338M PHE* 1.3 69.8 + - + +
340M ASN* 3.4 15.1 + - - +
341M ILE 4.0 0.2 + - - -
358M ARG 3.8 22.4 - - - +
359M SER* 4.1 1.6 - - - -
360M LEU* 3.9 40.3 - - + +
380M TYR* 3.4 35.8 - - + +
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Residues in contact with PHE 338 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334M VAL* 2.9 33.7 + - + +
335M LEU* 4.9 0.7 - - - -
337M LEU* 1.3 89.3 - - + +
339M SER* 1.3 59.4 + - - +
341M ILE* 3.1 30.0 + - + +
344M ALA* 3.6 9.2 - - - +
349M ALA* 3.7 32.3 - - + -
352M TRP* 3.9 30.3 - + + -
353M TYR* 4.1 4.0 - - + -
357M PHE* 3.4 35.9 - - + -
358M ARG 3.7 3.8 - - - -
359M SER 3.7 16.8 - - - -
360M LEU* 4.5 2.7 - - + -
363M ILE* 3.4 30.5 - - + -
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Residues in contact with SER 339 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265M LYS* 4.9 4.2 + - - -
269M VAL* 4.0 14.5 - - - +
335M LEU 2.9 23.2 + - - -
336M GLU* 3.5 9.4 + - - -
338M PHE* 1.3 73.6 - - - +
340M ASN* 1.3 57.6 + - - +
341M ILE 3.1 5.2 - - - -
344M ALA 3.4 15.9 - - - -
345M GLY* 4.2 17.3 - - - -
346M THR* 4.7 2.7 - - - -
349M ALA* 4.2 2.9 - - - +
601M NA 2.4 25.3 - - - -
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Residues in contact with ASN 340 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265M LYS* 4.4 10.0 + - - -
336M GLU* 2.9 44.0 + - - +
337M LEU* 3.4 3.2 - - - +
338M PHE 3.2 0.4 - - - -
339M SER* 1.3 78.3 + - - +
341M ILE* 1.3 59.5 + - - +
342M TRP 3.5 2.8 + - - -
376M GLY 5.6 0.3 - - - +
380M TYR* 3.2 40.3 + - + +
383M PHE* 5.8 3.8 - - - +
384M LEU* 4.0 30.8 - - + +
601M NA 4.3 0.2 - - - -
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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