Contacts of the helix formed by residues 4505 - 4519 (chain L) in PDB entry 2ZLE
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 SER4505 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4421L MET* 4.4 9.6 - - - +
4422L ALA 2.7 24.5 + - - -
4424L SER* 2.5 23.5 + - - -
4482L LEU* 3.2 31.8 + - - -
4483L ILE* 2.6 19.2 + - - -
4484L GLY 4.0 0.9 - - - +
4503L ILE 3.6 0.2 + - - -
4504L PRO* 1.3 70.1 - - - +
4506L ASN* 1.3 53.7 + - - -
4508L VAL* 3.1 12.8 + - - +
4509L LYS* 2.9 29.0 + - - +
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Residues in contact with ASN4506 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4422L ALA 3.5 11.7 + - - -
4423L ASP* 2.5 27.5 + - - +
4424L SER* 2.5 38.6 + - - +
4425L ASP* 3.3 19.4 + - - +
4504L PRO* 5.4 0.2 - - + -
4505L SER* 1.3 71.5 - - - +
4507L MET* 1.3 62.1 + - - +
4509L LYS* 3.5 19.2 + - - +
4510L ASN* 3.2 22.3 + - - +
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Residues in contact with MET4507 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4403L SER* 5.8 1.1 - - - -
4503L ILE* 3.7 20.6 - - + -
4504L PRO* 2.9 21.8 + - + +
4506L ASN* 1.3 76.1 - - - +
4508L VAL* 1.3 61.5 + - - +
4510L ASN* 3.2 18.5 + - + +
4511L LEU* 2.8 52.9 + - + +
4523L ARG* 5.6 2.7 - - - -
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Residues in contact with VAL4508 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4362L ILE* 6.0 1.1 - - + -
4370L VAL* 3.7 32.3 - - + -
4405L ILE* 4.3 11.6 - - + +
4421L MET* 5.2 5.4 - - - -
4482L LEU* 5.1 4.7 - - + -
4485L ILE* 4.2 18.4 - - + +
4503L ILE* 3.8 21.3 - - + +
4504L PRO 2.9 22.9 - - - +
4505L SER* 3.1 10.1 + - - +
4507L MET* 1.3 77.2 - - - +
4509L LYS* 1.3 60.2 + - - +
4511L LEU* 4.2 7.9 - - - +
4512L THR* 2.8 34.5 + - + -
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Residues in contact with LYS4509 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4421L MET* 4.1 42.3 + - + +
4422L ALA 5.9 0.4 - - - -
4505L SER 2.9 12.4 + - - +
4506L ASN* 3.6 22.9 - - - +
4507L MET 3.3 0.2 - - - -
4508L VAL* 1.3 75.1 - - - +
4510L ASN* 1.3 58.7 + - - +
4512L THR* 3.1 10.7 - - + +
4513L SER* 3.0 39.5 + - - +
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Residues in contact with ASN4510 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4506L ASN 3.2 11.4 + - - +
4507L MET* 3.2 27.4 + - + +
4509L LYS* 1.3 80.4 - - - +
4511L LEU* 1.3 67.6 + - - +
4512L THR 3.4 0.2 + - - -
4513L SER* 3.6 4.5 + - - -
4514L GLN* 3.4 41.4 + - - +
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Residues in contact with LEU4511 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4400L ASP* 3.3 22.7 - - + +
4403L SER* 3.4 27.6 - - - +
4405L ILE* 4.2 19.5 - - + -
4503L ILE* 4.7 1.6 - - + -
4507L MET* 2.8 47.8 + - + +
4508L VAL* 4.2 3.1 - - - +
4510L ASN* 1.3 78.3 - - - +
4512L THR* 1.3 60.7 + - - +
4514L GLN* 3.4 2.5 + - - +
4515L MET* 3.0 34.0 + - + +
4521L VAL* 3.4 22.6 - - + +
4523L ARG* 3.5 18.2 - - - +
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Residues in contact with THR4512 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4362L ILE* 4.8 16.8 - - + +
4370L VAL* 4.4 12.3 - - - +
4405L ILE* 5.3 3.4 - - - +
4407L LEU* 3.3 29.6 - - + +
4421L MET* 5.7 3.6 - - + -
4508L VAL* 2.8 19.9 + - + +
4509L LYS* 3.1 18.4 - - + +
4511L LEU* 1.3 76.7 - - - +
4513L SER* 1.3 71.5 + - - +
4515L MET* 3.2 20.2 + - - +
4516L VAL* 3.2 15.7 + - + +
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Residues in contact with SER4513 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4509L LYS* 3.0 22.2 + - - +
4510L ASN* 4.0 6.0 - - - -
4511L LEU 3.4 0.2 - - - -
4512L THR* 1.3 78.4 - - - +
4514L GLN* 1.3 66.9 + - - +
4516L VAL* 3.1 9.4 + - - +
4517L GLU* 2.9 46.3 + - - +
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Residues in contact with GLN4514 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4510L ASN* 3.4 34.0 + - - +
4511L LEU* 3.4 10.5 + - - +
4512L THR 3.2 0.4 - - - -
4513L SER* 1.3 80.2 - - - +
4515L MET* 1.3 65.3 + - - +
4518L TYR* 3.0 43.5 + - + +
4520L GLN 3.4 10.6 - - - +
4521L VAL* 2.9 18.8 - - + +
4522L LYS* 2.6 41.3 + - - +
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Residues in contact with MET4515 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4397L VAL* 4.1 4.3 - - + +
4398L GLY* 3.3 37.2 - - - +
4399L LYS 3.3 31.0 - - - +
4400L ASP* 3.5 13.5 - - + +
4405L ILE* 3.4 23.1 - - + +
4406L ALA 4.3 1.1 - - - -
4407L LEU* 3.7 23.3 - - + -
4511L LEU* 3.0 21.5 - - + +
4512L THR* 3.2 10.9 + - - +
4514L GLN* 1.3 74.7 - - - +
4516L VAL* 1.3 60.6 + - - +
4519L GLY* 2.9 26.7 + - - -
4520L GLN* 4.1 12.1 - - - +
4521L VAL* 4.3 10.5 - - + +
4678L ARG* 3.8 6.9 + - - -
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Residues in contact with VAL4516 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4366L LYS* 5.7 2.5 - - - +
4368L TYR* 3.8 42.0 - - + +
4397L VAL* 4.6 7.1 - - + +
4407L LEU* 3.9 15.0 - - + -
4512L THR* 3.2 11.5 + - + +
4513L SER* 3.1 12.6 + - - +
4515L MET* 1.3 82.3 - - - +
4517L GLU* 1.3 71.7 + - + +
4518L TYR 3.3 3.6 + - - -
4675L ALA* 3.3 14.4 - - - +
4678L ARG* 4.7 2.9 + - - -
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Residues in contact with GLU4517 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4513L SER* 2.9 35.7 + - - +
4514L GLN 3.7 0.2 - - - -
4516L VAL* 1.3 81.4 - - + +
4518L TYR* 1.3 90.7 + - + +
4673L ASN* 4.1 4.2 + - - -
4675L ALA* 3.5 10.0 - - - +
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Residues in contact with TYR4518 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4514L GLN* 3.0 41.4 + - + +
4516L VAL 3.3 1.2 + - - -
4517L GLU* 1.3 104.7 + - + +
4519L GLY* 1.3 61.7 + - - +
4520L GLN 3.3 11.2 - - - +
4522L LYS* 4.1 31.9 - - + -
4634L ASN* 3.1 23.8 + - - +
4638L ASP* 5.2 8.1 - - - -
4673L ASN* 3.8 18.7 - - + +
4674L ILE 3.5 6.8 + - - -
4675L ALA* 3.3 19.7 + - - +
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Residues in contact with GLY4519 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4397L VAL 3.9 10.0 - - - +
4398L GLY* 4.7 3.5 - - - -
4515L MET* 2.9 20.2 + - - -
4518L TYR* 1.3 79.8 - - - +
4520L GLN* 1.3 58.9 + - - +
4621L ASN* 2.7 25.4 - - - +
4634L ASN* 4.6 0.7 - - - -
4674L ILE* 3.9 11.9 - - - -
4675L ALA* 4.0 2.3 - - - +
4678L ARG* 3.4 17.7 - - - -
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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