Contacts of the helix formed by residues 484 - 493 (chain 8) in PDB entry 6FF7
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 ASP 484 (chain 8).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4828 ALA* 4.1 2.5 - - - +
4838 GLN* 1.3 81.1 - - + +
4858 PRO* 1.3 63.9 - - - +
4868 LYS 3.3 4.2 + - - +
4878 LEU* 3.8 9.9 + - + +
4888 LEU* 3.4 18.4 + - - +
1255u PHE* 4.9 11.3 - - + +
28x LYS* 5.3 14.1 - - + +
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Residues in contact with PRO 485 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4658 LEU* 5.8 8.3 - - + -
4798 ASP* 3.6 25.9 - - + +
4808 VAL* 5.0 7.2 - - - +
4828 ALA* 4.6 6.1 - - + +
4848 ASP* 1.3 72.7 - - - +
4868 LYS* 1.3 57.5 + - - +
4878 LEU 3.5 0.2 - - - -
4888 LEU* 3.4 9.3 - - + +
4898 VAL* 2.9 30.8 + - - +
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Residues in contact with LYS 486 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4848 ASP 3.3 1.0 - - - -
4858 PRO* 1.3 79.3 - - - +
4878 LEU* 1.3 58.7 + - - +
4898 VAL* 3.4 3.8 + - - +
4908 HIS* 2.9 27.3 + - - +
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Residues in contact with LEU 487 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4848 ASP* 3.8 12.4 + - + +
4858 PRO 3.5 0.2 - - - -
4868 LYS* 1.3 76.1 - - - +
4888 LEU* 1.3 59.5 + - - +
4908 HIS* 3.7 8.1 - - + +
4918 LEU* 2.9 30.5 + - - +
28x LYS* 5.9 6.7 - - + -
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Residues in contact with LEU 488 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4798 ASP* 5.7 5.6 - - + +
4828 ALA* 5.0 5.4 - - + -
4848 ASP 3.4 14.1 + - - +
4858 PRO* 3.4 13.9 + - + +
4868 LYS 3.2 0.6 - - - -
4878 LEU* 1.3 78.8 - - - +
4898 VAL* 1.3 56.9 + - - +
4918 LEU* 3.4 4.7 + - - +
4928 LYS* 2.9 26.6 + - - +
1252u GLN* 5.0 3.0 - - - +
1255u PHE* 4.8 21.6 - - + +
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Residues in contact with VAL 489 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4658 LEU 5.8 2.2 - - - +
4698 VAL* 5.3 14.1 - - + -
4718 ARG 5.5 3.4 - - - +
4748 VAL* 6.1 0.2 - - - +
4758 VAL* 5.3 15.5 - - + -
4798 ASP* 6.1 4.7 - - + -
4858 PRO 2.9 16.8 + - - +
4868 LYS* 3.8 3.4 - - - +
4888 LEU* 1.3 73.9 - - - +
4908 HIS* 1.3 59.4 + - - +
4928 LYS* 3.6 11.7 - - + +
4938 ALA* 3.1 26.3 + - - +
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Residues in contact with HIS 490 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4868 LYS 2.9 17.3 + - - +
4878 LEU* 3.7 10.3 - - + +
4888 LEU 3.2 0.6 - - - -
4898 VAL* 1.3 78.7 - - - +
4918 LEU* 1.3 58.0 + - - +
4928 LYS 3.2 0.2 - - - -
4938 ALA* 3.0 8.0 + - - +
4948 THR* 2.9 25.3 + - - -
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Residues in contact with LEU 491 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4878 LEU 2.9 17.9 + - - +
4888 LEU* 3.7 4.5 - - - +
4908 HIS* 1.3 74.9 - - - +
4928 LYS* 1.3 61.3 + - - +
4938 ALA 3.2 0.2 - - - -
4948 THR* 3.7 17.8 + - - -
4978 SER* 4.5 8.1 - - - -
1251u LEU* 5.0 5.8 - - + +
1252u GLN* 3.3 34.3 + - - +
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Residues in contact with LYS 492 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4748 VAL* 4.3 25.5 - - + +
4888 LEU 2.9 18.4 + - - +
4898 VAL* 3.7 13.0 - - + +
4908 HIS 3.2 0.2 - - - -
4918 LEU* 1.3 77.6 - - - +
4938 ALA* 1.3 57.3 + - - +
4948 THR 3.5 2.4 - - - +
1252u GLN* 4.1 11.4 - - + +
1083v ASN* 5.7 1.0 - - - +
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Residues in contact with ALA 493 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4718 ARG* 4.2 27.1 - - + +
4748 VAL* 5.7 3.6 - - + -
4898 VAL 3.1 15.2 + - - +
4908 HIS* 3.0 9.8 + - - +
4928 LYS* 1.3 78.1 - - - +
4948 THR* 1.3 61.6 + - - +
1083v ASN* 4.3 11.0 - - - +
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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