Contacts of the helix formed by residues 331 - 340 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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270I GLN* 4.9 2.3 + - - -
329I SER* 2.9 20.9 + - - -
330I GLU* 1.3 77.7 - - - +
332I VAL* 1.3 66.2 + - - +
333I PRO 3.4 0.2 - - - -
334I VAL* 3.1 6.6 + - - +
335I LEU* 2.9 39.4 + - - +
353I TYR* 3.5 43.0 + - - -
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Residues in contact with VAL 332 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265I LYS* 5.4 0.9 - - + -
266I ALA* 4.0 18.8 - - + +
269I VAL* 3.9 13.6 - - + +
270I GLN* 3.7 38.8 - - + +
328I ILE* 3.7 18.2 - - + -
329I SER 3.1 15.0 + - - +
331I SER* 1.3 77.1 + - - +
333I PRO* 1.4 68.6 - - + +
335I LEU* 3.2 8.5 + - - +
336I GLU* 2.8 35.3 + - - +
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Residues in contact with PRO 333 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328I ILE* 5.9 0.4 - - + -
329I SER 4.0 2.2 - - - +
330I GLU* 3.2 21.3 - - - +
332I VAL* 1.4 96.6 - - + +
334I VAL* 1.3 58.8 + - + +
336I GLU* 3.5 9.7 + - + +
337I LEU* 3.0 24.3 + - - +
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Residues in contact with VAL 334 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330I GLU 4.3 11.0 - - - +
331I SER 3.1 7.1 + - - +
333I PRO* 1.3 75.0 - - + +
335I LEU* 1.3 68.9 + - - +
336I GLU 3.2 0.4 - - - -
337I LEU* 3.2 7.7 + - - +
338I PHE* 2.9 47.5 + - + -
353I TYR* 3.4 36.3 - - + -
357I PHE 4.2 3.4 - - - +
358I ARG* 3.8 26.0 - - + +
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Residues in contact with LEU 335 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269I VAL* 4.1 26.3 - - + +
270I GLN* 4.2 20.4 - - + -
331I SER* 2.9 39.6 + - - +
332I VAL* 3.6 4.7 - - - +
334I VAL* 1.3 78.4 - - + +
336I GLU* 1.3 60.7 + - - +
338I PHE* 3.4 0.4 + - - -
339I SER* 3.0 27.2 + - - -
349I ALA* 3.5 40.9 - - + +
350I GLN* 3.9 15.0 - - + +
353I TYR* 4.0 17.7 - - + -
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Residues in contact with GLU 336 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265I LYS* 3.1 39.8 - - + +
269I VAL* 3.6 21.8 - - + +
332I VAL* 2.8 22.9 + - - +
333I PRO* 3.6 9.9 - - + +
334I VAL 3.2 0.2 - - - -
335I LEU* 1.3 74.1 - - - +
337I LEU* 1.3 66.1 + - - +
339I SER* 3.3 3.2 + - - +
340I ASN* 2.9 45.5 + - - +
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Residues in contact with LEU 337 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333I PRO 3.0 14.5 + - - +
334I VAL* 3.3 10.5 - - - +
336I GLU* 1.3 77.9 - - - +
338I PHE* 1.3 69.9 + - + +
340I ASN* 3.2 18.7 + - - +
341I ILE* 4.2 1.6 - - - +
358I ARG 3.8 21.8 - - - +
359I SER* 4.0 1.8 - - - -
360I LEU* 3.8 42.9 - - + +
380I TYR* 3.3 33.5 - - + +
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Residues in contact with PHE 338 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334I VAL* 2.9 29.4 + - + +
335I LEU* 5.0 0.2 - - - -
337I LEU* 1.3 90.5 - - + +
339I SER* 1.3 58.1 + - - +
341I ILE* 3.0 33.4 + - - +
344I ALA* 3.7 7.5 - - - +
349I ALA* 3.7 35.0 - - + -
352I TRP* 3.7 30.3 - + + -
353I TYR 4.1 4.0 - - - -
357I PHE 3.5 33.0 - - - -
358I ARG* 3.7 8.1 - - - -
359I SER 3.8 14.6 - - - -
360I LEU* 4.7 2.2 - - + -
363I ILE* 3.6 31.0 - - + -
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Residues in contact with SER 339 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269I VAL* 3.8 14.7 - - - +
335I LEU 3.0 19.0 + - - -
336I GLU* 3.3 9.9 + - - +
338I PHE* 1.3 71.4 - - - +
340I ASN* 1.3 56.5 + - - +
341I ILE 3.1 5.4 - - - -
344I ALA 3.3 17.5 - - - -
345I GLY* 4.3 17.0 - - - -
346I THR* 4.7 2.7 - - - -
349I ALA* 4.2 3.1 - - - +
601I NA 2.3 26.5 - - - -
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Residues in contact with ASN 340 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336I GLU* 2.9 38.9 + - - +
337I LEU* 3.3 7.2 - - - +
338I PHE 3.1 0.6 - - - -
339I SER* 1.3 78.1 + - - +
341I ILE* 1.3 59.6 + - - +
342I TRP 3.6 2.8 + - - -
376I GLY 5.5 0.3 - - - +
380I TYR* 3.1 40.7 + - + +
383I PHE* 5.8 4.2 - - - +
384I LEU* 4.0 31.1 - - + +
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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