Contacts of the helix formed by residues 4540 - 4553 (chain D) in PDB entry 2H7C
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 LYS4540 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4350D ILE* 3.7 23.7 - - + +
4352D LYS 5.2 6.7 + - - -
4419D ASP* 6.2 1.6 - - - +
4423D ASP* 2.8 32.0 + - - +
4427D GLY* 4.3 20.4 - - - +
4431D VAL* 4.0 8.7 - - + -
4448D GLU* 4.2 13.6 + - - -
4538D LYS 3.2 1.8 + - - -
4539D LEU* 1.3 86.0 - - + +
4541D ASP* 1.3 63.7 + - - +
4543D GLU* 3.2 35.4 + - + +
4544D VAL* 2.9 27.6 + - + +
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Residues in contact with ASP4541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4435D ARG* 2.9 29.2 + - - +
4524D GLU* 4.7 0.4 - - - -
4538D LYS* 3.1 45.7 + - + +
4539D LEU 3.0 5.2 + - - -
4540D LYS* 1.3 76.4 - - - +
4542D LYS* 1.3 65.3 + - + +
4543D GLU* 3.8 0.4 + - - -
4544D VAL* 3.4 2.3 + - - +
4545D ALA* 3.2 22.2 + - - +
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Residues in contact with LYS4542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4402D LYS* 6.0 0.4 - - - -
4540D LYS 3.4 0.6 - - - -
4541D ASP* 1.3 79.0 - - + +
4543D GLU* 1.3 70.7 + - - +
4545D ALA* 3.4 6.7 + - - +
4546D PHE* 3.0 28.6 + - - +
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Residues in contact with GLU4543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4403D TYR* 3.5 14.3 - - + +
4423D ASP* 3.3 26.4 - - - +
4428D VAL* 4.0 11.9 - - + -
4540D LYS* 3.2 39.3 + - + +
4541D ASP 3.8 0.3 + - - -
4542D LYS* 1.3 86.3 + - - +
4544D VAL* 1.3 66.1 + - - +
4546D PHE* 3.3 4.2 + - - -
4547D TRP* 3.0 32.6 + - - -
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Residues in contact with VAL4544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4428D VAL* 4.1 25.1 - - + +
4431D VAL* 3.8 32.1 - - + -
4432D ILE* 4.0 17.9 - - + -
4435D ARG* 3.6 21.8 - - - +
4540D LYS* 2.9 21.4 + - + +
4541D ASP 3.8 4.9 - - - +
4543D GLU* 1.3 75.0 - - - +
4545D ALA* 1.3 57.0 + - - +
4547D TRP* 4.3 0.2 - - - +
4548D THR* 2.6 47.8 + - - +
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Residues in contact with ALA4545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4435D ARG* 5.7 0.2 - - - +
4541D ASP* 3.2 12.4 + - - +
4542D LYS* 3.6 9.2 - - - +
4543D GLU 3.2 0.4 - - - -
4544D VAL* 1.3 80.3 - - - +
4546D PHE* 1.3 64.4 + - - +
4548D THR* 4.0 3.3 - - - -
4549D ASN* 2.9 40.0 + - - +
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Residues in contact with PHE4546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4398D GLU* 4.3 11.0 - - + -
4399D ALA* 4.2 8.1 - - - -
4402D LYS* 3.5 57.7 - - + -
4403D TYR* 4.4 3.8 - + - -
4542D LYS 3.0 17.1 + - - +
4543D GLU* 3.7 5.6 - - - +
4545D ALA* 1.3 78.0 - - - +
4547D TRP* 1.3 98.5 + + - +
4549D ASN* 3.9 5.0 - - - +
4550D LEU* 3.0 54.8 + - + +
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Residues in contact with TRP4547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4391D ILE* 3.7 22.9 - - + -
4399D ALA* 3.8 12.6 - - + -
4403D TYR* 2.9 37.2 + + - -
4420D LEU* 3.2 35.9 - - + -
4423D ASP* 4.2 5.0 - - + +
4424D VAL* 3.5 17.3 - - + -
4428D VAL* 3.6 29.6 - - + -
4543D GLU 3.0 28.0 + - - +
4544D VAL 4.3 0.9 - - - +
4546D PHE* 1.3 84.9 - + - +
4548D THR* 1.3 68.0 + - - +
4550D LEU* 3.6 26.2 - - + +
4551D PHE* 2.9 59.6 + + + -
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Residues in contact with THR4548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4428D VAL* 5.2 0.9 - - - +
4432D ILE* 4.3 11.8 - - + +
4544D VAL* 2.6 36.0 + - - +
4545D ALA* 4.0 4.0 - - - -
4547D TRP* 1.3 76.2 - - - +
4549D ASN* 1.3 62.7 + - - +
4551D PHE* 3.6 5.5 + - - +
4552D ALA* 3.0 30.9 + - + +
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Residues in contact with ASN4549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4545D ALA* 2.9 30.6 + - - +
4546D PHE* 3.9 4.7 - - - +
4548D THR* 1.3 79.9 - - - +
4550D LEU* 1.3 66.5 + - - +
4552D ALA* 3.2 15.5 + - - +
4553D LYS* 3.4 10.6 + - - +
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Residues in contact with LEU4550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4391D ILE* 5.3 0.9 - - + -
4395D LEU* 4.0 37.9 - - + +
4398D GLU* 3.3 37.0 - - + +
4399D ALA* 4.1 12.6 - - + -
4546D PHE* 3.0 37.3 + - + +
4547D TRP* 3.1 35.2 + - + +
4549D ASN* 1.3 76.5 - - - +
4551D PHE* 1.3 64.8 + - + +
4553D LYS* 3.2 24.4 + - + +
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Residues in contact with PHE4551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4389D VAL 4.2 15.7 - - - -
4390D CYS 3.9 17.7 - - - -
4391D ILE* 4.2 13.0 - - + -
4395D LEU* 4.5 16.6 - - + -
4424D VAL* 4.5 10.1 - - + -
4547D TRP* 2.9 58.8 + + + +
4548D THR* 4.1 4.3 - - - +
4550D LEU* 1.3 75.9 - - + +
4552D ALA* 1.3 57.9 + - - +
4553D LYS 3.2 6.9 + - - -
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Residues in contact with ALA4552 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4548D THR* 3.0 21.8 + - + +
4549D ASN* 3.6 10.8 - - - +
4550D LEU 3.2 0.6 - - - -
4551D PHE* 1.3 76.5 - - - +
4553D LYS* 1.3 63.4 + - - +
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Residues in contact with LYS4553 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4394D GLU* 5.3 13.1 + - - +
4395D LEU* 3.9 25.2 - - + +
4398D GLU* 4.3 16.9 + - - +
4549D ASN 3.4 6.2 + - - +
4550D LEU* 3.2 18.5 + - + +
4551D PHE 3.2 4.9 - - - -
4552D ALA* 1.3 84.1 - - - +
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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