Contacts of the helix formed by residues 4544 - 4556 (chain D) in PDB entry 6X34
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 VAL4544 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4543D GLU* 1.3 78.5 - - + +
4545D GLN* 1.3 63.4 + - - +
4546D ARG 3.2 0.2 - - - -
4547D VAL* 3.3 15.7 - - + +
4548D LYS* 3.3 21.8 + - - +
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Residues in contact with GLN4545 (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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4543D GLU 3.2 7.0 - - - +
4544D VAL* 1.3 77.3 - - - +
4546D ARG* 1.3 59.6 + - - +
4548D LYS* 3.8 5.8 - - - +
4549D PHE* 3.0 28.6 + - - +
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Residues in contact with ARG4546 (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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4543D GLU 3.4 15.8 + - - +
4544D VAL 3.2 0.8 - - - -
4545D GLN* 1.3 77.2 - - - +
4547D VAL* 1.3 67.5 + - + +
4549D PHE* 3.4 10.1 + - - +
4550D LEU* 3.3 24.6 + - - +
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Residues in contact with VAL4547 (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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4543D GLU 4.1 8.9 + - - +
4544D VAL* 3.3 21.3 - - + +
4546D ARG* 1.3 79.8 - - + +
4548D LYS* 1.3 57.1 - - + +
4550D LEU* 3.8 10.9 + - + +
4551D ASN* 2.6 36.7 + - - +
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Residues in contact with LYS4548 (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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4544D VAL 3.3 14.7 + - - +
4545D GLN* 4.0 7.2 - - - +
4546D ARG 3.2 1.0 - - - -
4547D VAL* 1.3 81.1 - - + +
4549D PHE* 1.3 64.9 + - - +
4550D LEU 3.2 0.7 - - - -
4551D ASN* 3.5 6.4 + - - +
4552D TYR* 3.1 23.6 + - - +
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Residues in contact with PHE4549 (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 GLN 3.0 17.9 + - - +
4546D ARG* 3.4 7.4 + - - +
4548D LYS* 1.3 74.9 - - - +
4550D LEU* 1.3 76.1 + - + +
4552D TYR* 3.9 19.7 - + - +
4553D LEU* 3.2 32.8 + - + +
4654D LEU* 5.4 11.2 - - + -
4657D ILE* 5.0 15.0 - - + -
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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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4546D ARG 3.3 18.6 - - - +
4547D VAL* 4.1 11.9 - - + +
4548D LYS 3.2 0.8 - - - -
4549D PHE* 1.3 91.0 - - + +
4551D ASN* 1.3 61.3 + - - +
4553D LEU* 4.1 3.4 - - - +
4554D SER* 2.9 26.6 + - - -
4657D ILE* 5.5 12.1 - - + +
4658D GLY* 5.4 1.2 - - - -
4661D CYS* 4.2 31.3 - - - +
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Residues in contact with ASN4551 (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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4547D VAL* 2.6 29.7 + - - +
4548D LYS* 3.5 7.6 + - - +
4550D LEU* 1.3 76.3 - - - +
4552D TYR* 1.3 64.1 + - - +
4554D SER* 3.0 17.1 + - - -
4555D ARG* 3.2 15.6 + - - +
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Residues in contact with TYR4552 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4548D LYS 3.1 18.8 + - - +
4549D PHE* 3.9 21.3 - + - +
4550D LEU 3.3 0.2 - - - -
4551D ASN* 1.3 78.8 - - - +
4553D LEU* 1.3 65.6 + - + +
4555D ARG* 3.6 3.1 + - + +
4556D ASN* 3.3 53.5 + - + +
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Residues in contact with LEU4553 (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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4549D PHE* 3.2 32.5 + - + +
4550D LEU* 4.2 2.9 - - - +
4551D ASN 3.4 0.2 - - - -
4552D TYR* 1.3 79.4 - - + +
4554D SER* 1.3 60.8 + - - +
4556D ASN* 3.5 4.1 - - - +
4557D PHE* 3.0 28.8 + - - +
4560D LEU* 5.7 4.7 - - + +
4654D LEU* 4.5 11.7 - - + +
4657D ILE* 5.1 1.8 - - + -
4658D GLY* 4.1 22.2 - - - +
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Residues in contact with SER4554 (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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4550D LEU 2.9 21.2 + - - -
4551D ASN* 3.0 18.5 + - - -
4553D LEU* 1.3 74.2 - - - +
4555D ARG* 1.3 61.7 + - - +
4557D PHE* 3.5 18.1 + - - +
4558D TYR* 4.9 1.0 + - - -
4658D GLY* 4.2 16.3 - - - -
4661D CYS* 4.4 18.2 - - - +
4662D LEU* 4.1 11.9 - - - +
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Residues in contact with ARG4555 (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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4551D ASN 3.2 16.5 + - - +
4552D TYR* 4.0 3.8 - - + +
4554D SER* 1.3 81.0 + - - +
4556D ASN* 1.3 67.2 + - - +
4557D PHE 3.3 2.6 + - - -
4558D TYR* 4.6 6.9 + - - +
4559D THR* 4.8 1.4 + - - +
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Residues in contact with ASN4556 (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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4552D TYR* 3.3 51.6 + - + +
4553D LEU* 3.5 5.4 - - - +
4555D ARG* 1.3 84.8 - - - +
4557D PHE* 1.3 57.1 + - - +
4558D TYR 3.4 0.7 - - - -
4559D THR* 3.0 26.1 + - - +
4560D LEU* 3.0 22.0 + - + +
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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