Contacts of the helix formed by residues 310 - 321 (chain B) in PDB entry 4Z2C
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 ALA 310 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246B ILE* 5.4 11.7 - - + -
254B GLU* 4.3 24.0 - - + -
256B ILE* 5.5 9.7 - - + +
304B VAL* 5.0 12.1 - - + +
309B SER* 1.3 75.5 - - - +
311B ASN* 1.3 60.2 + - - +
313B ILE* 3.2 7.9 + - - +
314B LEU* 2.9 31.2 + - - +
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Residues in contact with ASN 311 (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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309B SER 3.4 0.8 - - - -
310B ALA* 1.3 76.8 - - - +
312B VAL* 1.3 60.0 + - + +
314B LEU* 3.9 4.5 - - - +
315B ASN* 2.9 30.5 + - - +
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Residues in contact with VAL 312 (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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309B SER* 3.3 23.8 + - - +
310B ALA 3.3 0.4 - - - -
311B ASN* 1.3 78.3 - - + +
313B ILE* 1.3 58.7 + - - +
315B ASN* 3.4 6.3 + - - +
316B ASN* 2.9 50.0 + - - +
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Residues in contact with ILE 313 (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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283B ILE* 6.0 1.4 - - - +
284B GLU 4.8 13.5 - - - +
285B GLY* 6.1 1.3 - - - -
304B VAL* 5.1 12.1 - - + -
309B SER* 3.1 15.4 + - - +
310B ALA* 3.2 10.7 + - - +
312B VAL* 1.3 78.5 - - - +
314B LEU* 1.3 57.0 + - - +
316B ASN* 3.4 12.2 + - - +
317B LEU* 2.9 27.0 + - - +
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Residues in contact with LEU 314 (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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244B THR* 6.1 0.7 - - - +
256B ILE* 5.0 15.5 - - + -
310B ALA 2.9 16.1 + - - +
311B ASN* 3.9 5.6 - - - +
313B ILE* 1.3 73.4 - - - +
315B ASN* 1.3 61.3 + - - +
317B LEU* 3.1 8.8 + - - +
318B PHE* 2.9 29.6 + - - +
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Residues in contact with ASN 315 (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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311B ASN 2.9 18.4 + - - +
312B VAL* 3.5 8.3 - - + +
314B LEU* 1.3 76.4 - - - +
316B ASN* 1.3 60.4 + - - +
318B PHE* 3.4 7.5 + - - +
319B LYS* 2.9 32.2 + - - +
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Residues in contact with ASN 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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282B ARG 5.4 6.6 + - - +
283B ILE* 5.6 11.9 - - + +
312B VAL* 2.9 43.0 + - - +
313B ILE* 3.4 11.5 - - - +
315B ASN* 1.3 75.2 - - - +
317B LEU* 1.3 59.8 + - - +
318B PHE 3.0 1.8 - - - -
319B LYS* 3.0 6.1 + - - +
320B MET* 2.9 35.3 + - + +
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Residues in contact with LEU 317 (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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313B ILE 2.9 16.7 + - - +
314B LEU* 3.1 10.7 + - - +
316B ASN* 1.3 74.7 - - - +
318B PHE* 1.3 58.7 + - - +
320B MET* 4.2 4.7 - - - -
321B THR* 3.7 15.7 - - - +
323B MET* 3.5 18.2 - - + +
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Residues in contact with PHE 318 (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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314B LEU 2.9 14.7 + - - +
315B ASN* 3.7 8.3 - - - +
317B LEU* 1.3 77.2 - - - +
319B LYS* 1.3 58.4 + - - +
320B MET 3.2 6.0 + - - -
321B THR* 4.2 6.9 + - - -
323B MET* 4.2 12.1 - - + +
324B GLN* 3.5 39.0 - - + +
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Residues in contact with LYS 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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315B ASN* 2.9 24.1 + - - +
316B ASN* 3.0 7.1 + - - +
318B PHE* 1.3 75.3 - - - +
320B MET* 1.3 60.2 + - - +
321B THR 5.4 0.4 - - - -
324B GLN* 5.1 2.5 - - - -
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Residues in contact with MET 320 (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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273B HIS* 4.5 10.7 - - + -
277B LEU* 5.8 7.4 - - + -
316B ASN* 2.9 17.3 + - + +
317B LEU* 4.5 5.6 - - - +
318B PHE 3.2 0.4 - - - -
319B LYS* 1.3 79.9 - - - +
321B THR* 1.3 74.1 + - + +
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Residues in contact with THR 321 (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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270B VAL* 5.4 14.4 - - + +
273B HIS* 4.4 24.1 - - + +
274B ILE* 5.9 5.4 - - + -
317B LEU* 3.7 15.7 + - - +
318B PHE 4.2 4.4 + - - -
319B LYS 5.4 0.4 - - - -
320B MET* 1.3 83.8 - - + +
323B MET* 3.0 39.8 + - + +
324B GLN 3.5 16.5 + - - -
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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