Contacts of the helix formed by residues 828 - 844 (chain U) 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 GLY 828 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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826U GLY* 3.2 5.9 + - - -
827U THR* 1.3 80.1 - - - +
829U LYS* 1.3 64.2 + - - +
830U THR* 3.2 3.8 - - - -
831U ASP* 3.4 11.3 + - - +
832U VAL* 3.1 23.7 + - - +
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Residues in contact with LYS 829 (chain U).
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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823U GLY* 5.2 18.3 - - - +
824U PRO 6.1 0.4 - - - +
827U THR* 3.6 3.0 - - - +
828U GLY* 1.3 76.5 - - - +
830U THR* 1.3 58.3 + - - +
832U VAL* 3.5 6.9 + - - +
833U ALA* 3.0 27.6 + - - +
1094U ILE* 5.1 18.6 - - + +
1095U GLY 6.2 0.2 - - - +
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Residues in contact with THR 830 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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828U GLY* 3.2 1.0 - - - -
829U LYS* 1.3 78.6 - - - +
831U ASP* 1.3 61.2 + - - +
833U ALA* 3.2 7.5 + - - +
834U VAL* 3.0 29.6 + - - +
861U GLN* 5.1 20.9 - - - -
862U LEU* 5.6 4.9 - - - -
865U LYS* 5.4 6.0 - - - +
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Residues in contact with ASP 831 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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800U ILE* 4.9 17.9 - - + -
828U GLY* 3.4 13.4 + - - +
830U THR* 1.3 75.3 - - - +
832U VAL* 1.3 66.4 + - - +
834U VAL* 4.1 4.0 - - - +
835U GLN* 3.2 25.1 + - - +
865U LYS* 5.9 3.1 - - - -
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Residues in contact with VAL 832 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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806U GLN* 5.2 13.9 - - + +
809U ALA* 5.0 15.9 - - + -
810U ILE* 5.3 7.3 - - - +
828U GLY 3.1 13.0 + - - +
829U LYS* 3.6 11.2 - - - +
831U ASP* 1.3 76.6 - - - +
833U ALA* 1.3 63.3 + - - +
835U GLN* 3.4 5.3 + - - +
836U ILE* 3.0 23.8 + - - +
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Residues in contact with ALA 833 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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829U LYS 3.0 15.0 + - - +
830U THR* 3.2 12.1 + - - +
832U VAL* 1.3 76.7 - - - +
834U VAL* 1.3 57.8 + - - +
836U ILE* 3.2 7.6 + - - +
837U ILE* 2.9 27.3 + - - +
862U LEU* 6.2 4.5 - - + -
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Residues in contact with VAL 834 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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830U THR 3.0 15.9 + - - +
831U ASP* 4.4 3.1 - - - +
833U ALA* 1.3 77.0 - - - +
835U GLN* 1.3 58.8 + - - +
837U ILE* 3.7 8.0 - - - +
838U SER* 2.8 30.0 + - - -
862U LEU* 4.8 7.9 - - + +
865U LYS* 4.5 21.5 - - + +
866U ILE* 4.7 13.9 - - + +
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Residues in contact with GLN 835 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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717U THR* 6.1 6.1 - - - -
810U ILE* 5.2 11.9 - - + -
831U ASP 3.2 19.1 + - - +
832U VAL* 3.7 5.4 - - - +
834U VAL* 1.3 75.8 - - - +
836U ILE* 1.3 59.2 + - - +
838U SER* 3.7 5.7 - - - -
839U ASN* 2.8 31.8 + - - +
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Residues in contact with ILE 836 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809U ALA 5.7 0.4 - - - +
810U ILE* 5.1 15.8 - - - +
813U GLY* 4.9 21.9 - - - +
814U MET* 5.9 1.7 - - - +
832U VAL 3.0 13.4 + - - +
833U ALA* 3.2 10.7 + - - +
835U GLN* 1.3 76.3 - - - +
837U ILE* 1.3 57.0 + - - +
839U ASN* 3.3 5.5 + - - +
840U ILE* 2.9 31.9 + - - +
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Residues in contact with ILE 837 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833U ALA 2.9 16.4 + - - +
834U VAL* 3.7 9.0 - - - +
836U ILE* 1.3 77.1 - - - +
838U SER* 1.3 56.8 + - - +
840U ILE* 3.5 5.9 + - - +
841U TYR* 2.9 29.4 + - - +
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Residues in contact with SER 838 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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834U VAL 2.8 21.7 + - - -
835U GLN* 3.7 6.7 - - - -
837U ILE* 1.3 74.7 - - - +
839U ASN* 1.3 61.7 + - - +
841U TYR* 3.2 9.0 + - - +
842U HIS* 3.1 24.3 + - - +
869U LEU* 5.0 17.0 - - - -
870U ASP 6.1 1.8 - - - -
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Residues in contact with ASN 839 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713U ASP 5.0 12.6 - - - +
714U PHE* 5.6 7.2 - - - +
715U ASN* 5.9 5.4 - - + -
810U ILE* 5.9 1.8 - - + +
814U MET* 5.1 15.0 - - + -
835U GLN 2.8 19.2 + - - +
836U ILE* 3.7 5.8 - - - +
838U SER* 1.3 76.3 - - - +
840U ILE* 1.3 58.5 - - - +
842U HIS* 3.5 3.7 + - - +
843U ASN* 2.9 33.1 + - - +
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Residues in contact with ILE 840 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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813U GLY 5.7 4.9 - - - +
814U MET* 5.9 6.8 - - - +
836U ILE 2.9 17.3 + - - +
837U ILE* 3.8 6.1 - - - +
839U ASN* 1.3 73.8 - - - +
841U TYR* 1.3 60.3 + - - +
843U ASN* 4.7 3.6 - - - -
844U PHE* 2.9 39.5 + - + +
847U GLN* 5.8 0.2 - - - +
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Residues in contact with TYR 841 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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837U ILE 2.9 19.3 + - - +
838U SER* 3.3 10.3 - - - +
840U ILE* 1.3 78.1 - - - +
842U HIS* 1.3 59.7 + - - +
844U PHE 5.0 1.3 - - - -
845U PRO* 3.7 21.5 - - - +
870U ASP 6.1 0.9 - - - +
871U ILE* 5.8 7.6 - - + -
1033U LYS* 6.3 4.0 - - + -
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Residues in contact with HIS 842 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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713U ASP* 6.5 0.2 - - - -
715U ASN* 5.3 13.0 - - + -
838U SER 3.1 15.4 + - - +
839U ASN* 4.2 3.8 - - - +
841U TYR* 1.3 75.9 - - + +
843U ASN* 1.3 65.4 + - - +
844U PHE 3.4 0.2 - - - -
845U PRO* 4.5 6.8 - - - +
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Residues in contact with ASN 843 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712U LEU* 6.3 1.1 - - + -
713U ASP* 4.9 22.0 - - + +
814U MET* 6.6 0.2 - - + -
839U ASN 2.9 19.1 + - - +
840U ILE* 4.4 2.5 - - - +
842U HIS* 1.3 77.6 - - - +
844U PHE* 1.3 62.0 + - + +
845U PRO 3.8 1.3 - - - -
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Residues in contact with PHE 844 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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840U ILE* 2.9 22.6 + - + +
841U TYR* 4.2 1.6 - - - +
843U ASN* 1.3 81.5 - - + +
845U PRO* 1.3 54.8 - - - +
846U GLU 3.1 5.6 - - - -
847U GLN* 3.0 36.7 + - + +
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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