Contacts of the helix formed by residues 4821 - 4830 (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 LEU4821 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4837B MET* 5.0 7.6 - - + +
4841B LEU* 3.6 34.1 - - + +
4815D ALA 3.8 14.6 - - - +
4818D VAL* 3.6 22.7 + - + +
4820D THR* 1.3 77.3 - - - +
4822D ARG* 1.3 63.9 + - - +
4823D THR 3.2 1.8 + - - -
4824D ILE* 3.3 18.8 + - - +
4825D LEU* 4.1 7.3 + - - +
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Residues in contact with ARG4822 (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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4815D ALA 5.5 0.2 + - - -
4816D MET* 6.1 4.3 - - + +
4817D GLY 5.8 2.9 - - - +
4818D VAL 3.2 18.1 + - - +
4819D LYS* 3.8 11.7 - - - +
4820D THR 3.2 1.0 - - - -
4821D LEU* 1.3 77.3 - - - +
4823D THR* 1.3 61.1 + - + +
4824D ILE 3.2 0.2 - - - -
4825D LEU* 3.6 9.0 + - - +
4826D SER* 3.3 22.6 + - - -
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Residues in contact with THR4823 (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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4819D LYS 3.5 18.2 - - - +
4820D THR* 3.2 12.9 + - - +
4822D ARG* 1.3 76.8 - - + +
4824D ILE* 1.3 63.9 + - - +
4826D SER* 3.8 5.6 - - - -
4827D SER* 3.0 32.6 + - - -
4938D PHE* 3.1 32.0 - - + -
4941D LEU* 5.3 14.9 - - + +
4942D ARG* 6.5 1.8 - - + -
4945D GLN* 6.2 4.0 - - + -
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Residues in contact with ILE4824 (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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4838B THR* 5.7 2.7 - - - -
4841B LEU* 3.7 26.9 - - + -
4925B ILE* 5.4 8.7 - - + -
4929B ILE* 3.8 44.4 - - + -
4820D THR 5.1 0.9 - - - +
4821D LEU* 3.3 9.8 + - - +
4822D ARG 3.2 0.8 - - - -
4823D THR* 1.3 84.0 - - - +
4825D LEU* 1.3 76.2 + - + +
4826D SER 3.3 0.5 + - - -
4827D SER* 3.5 3.2 + - - -
4828D VAL* 3.3 30.6 + - + +
4938D PHE* 4.6 7.6 - - + -
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Residues in contact with LEU4825 (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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4841B LEU* 6.5 2.2 - - + -
4812D LEU 5.6 5.4 - - - +
4815D ALA* 5.9 5.4 - - + -
4816D MET* 5.4 14.6 - - + +
4821D LEU 4.1 8.2 + - - +
4822D ARG* 3.6 9.2 + - - +
4823D THR 3.5 0.2 - - - -
4824D ILE* 1.3 87.3 - - + +
4826D SER* 1.3 61.4 + - - +
4828D VAL* 3.9 6.8 + - + +
4829D THR* 3.9 18.4 + - - -
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Residues in contact with SER4826 (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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4822D ARG 3.3 16.5 + - - -
4823D THR* 4.0 6.5 - - - -
4824D ILE 3.2 1.0 - - - -
4825D LEU* 1.3 77.9 - - - +
4827D SER* 1.3 54.6 + - - +
4828D VAL 3.2 0.2 - - - -
4829D THR* 3.2 5.7 + - - -
4830D HIS* 2.7 39.8 + - - +
4941D LEU* 4.2 17.5 - - - +
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Residues in contact with SER4827 (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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4823D THR 3.0 19.7 + - - -
4824D ILE* 4.2 4.5 - - - -
4826D SER* 1.3 77.1 - - - +
4828D VAL* 1.3 63.3 + - - +
4830D HIS* 3.4 21.6 - - - +
4934D ILE* 3.1 36.6 + - - +
4937D ALA* 3.5 12.1 - - - +
4938D PHE* 3.6 21.8 + - - +
4941D LEU* 5.1 4.5 - - - +
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Residues in contact with VAL4828 (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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4921B PHE* 4.8 23.3 - - + -
4925B ILE* 4.3 25.6 - - + -
4824D ILE* 3.3 21.5 + - + +
4825D LEU* 4.2 8.3 - - + +
4826D SER 3.2 0.8 - - - -
4827D SER* 1.3 79.6 - - - +
4829D THR* 1.3 63.4 + - - +
4830D HIS 4.2 2.3 - - - +
4832D GLY* 5.0 0.3 - - - -
4835D LEU* 3.6 28.2 - - + +
4934D ILE* 4.2 13.7 - - + +
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Residues in contact with THR4829 (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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4825D LEU 3.9 10.7 + - - -
4826D SER* 3.2 6.1 + - - -
4828D VAL* 1.3 81.6 - - - +
4830D HIS* 1.3 64.7 + - - +
4831D ASN 3.4 0.3 + - - -
4832D GLY* 3.0 18.2 + - - -
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Residues in contact with HIS4830 (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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4826D SER* 2.7 26.8 + - - +
4827D SER* 3.4 19.4 - - - +
4828D VAL 3.5 2.5 - - - +
4829D THR* 1.3 74.0 - - - +
4831D ASN* 1.3 81.2 + - + +
4835D LEU* 6.0 0.3 - - - +
4933D LEU 5.6 0.3 - - - +
4934D ILE* 5.5 1.7 - - - +
4937D ALA* 4.1 27.8 - - + +
4940D GLU* 6.1 3.3 - - + +
4941D LEU* 5.3 17.8 - - + +
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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