Contacts of the helix formed by residues 740 - 754 (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 740 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1211 SER 5.6 6.1 - - - -
1221 GLU* 5.8 5.8 - - - -
739u ARG* 1.3 75.5 - - - +
741u LYS* 1.3 64.9 + - - -
742u GLY 3.2 1.8 - - - -
743u LEU* 3.2 13.7 + - - +
744u ALA* 3.3 10.9 + - - +
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Residues in contact with LYS 741 (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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1221 GLU* 5.5 11.0 - - + +
703u THR* 5.2 2.3 - - - -
740u GLY* 1.3 69.3 - - - -
742u GLY* 1.3 60.6 + - - +
744u ALA* 3.2 9.3 + - + +
745u ALA* 2.9 28.8 + - - +
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Residues in contact with GLY 742 (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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699u GLN 6.0 0.4 - - - -
702u ARG 6.3 0.2 - - - -
703u THR* 5.1 10.3 - - - -
706u ALA* 5.5 0.3 - - - +
734u GLY 5.9 0.4 - - - -
738u HIS* 5.6 7.2 - - - -
739u ARG 5.1 1.3 + - - -
740u GLY* 3.2 1.4 - - - -
741u LYS* 1.3 76.7 - - - +
743u LEU* 1.3 58.0 + - - +
745u ALA* 3.8 5.4 - - - +
746u PHE* 2.9 31.1 + - - +
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Residues in contact with LEU 743 (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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734u GLY 5.2 3.4 - - - +
735u ILE* 5.7 6.1 - - + +
738u HIS 3.8 20.0 + - - +
739u ARG* 3.9 5.0 - - + +
740u GLY 3.2 24.4 + - - +
742u GLY* 1.3 74.9 - - - +
744u ALA* 1.3 59.2 + - - +
746u PHE* 3.8 5.3 - - - +
747u LEU* 2.9 31.0 + - - +
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Residues in contact with ALA 744 (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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740u GLY 3.3 8.2 + - - +
741u LYS* 3.2 13.0 + - - +
743u LEU* 1.3 78.8 - - - +
745u ALA* 1.3 56.7 + - - +
747u LEU* 3.4 5.8 + - - +
748u LYS* 2.9 28.4 + - - +
784u MET* 4.5 25.8 - - + -
787u ILE* 4.5 14.1 - - + +
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Residues in contact with ALA 745 (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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703u THR* 3.8 23.8 - - - +
706u ALA* 3.6 22.7 - - + +
707u LEU* 4.8 4.4 - - + +
741u LYS 2.9 15.4 + - - +
742u GLY 3.9 3.4 - - - +
744u ALA* 1.3 76.0 - - - +
746u PHE* 1.3 58.8 + - - +
748u LYS* 3.4 8.0 + - - +
749u ALA* 3.0 28.6 + - - +
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Residues in contact with PHE 746 (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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706u ALA* 4.0 10.2 - - + +
731u LEU* 4.5 26.0 - - - +
734u GLY* 5.0 4.5 - - - -
735u ILE* 4.9 13.0 - - + +
742u GLY 2.9 18.5 + - - +
743u LEU* 3.8 7.0 - - - +
745u ALA* 1.3 76.2 - - - +
747u LEU* 1.3 57.0 + - - +
749u ALA* 3.3 4.7 + - - +
750u ILE* 2.9 29.9 + - - +
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Residues in contact with LEU 747 (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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735u ILE* 6.0 3.3 - - + +
743u LEU 2.9 19.2 + - - +
744u ALA* 3.7 6.7 - - - +
746u PHE* 1.3 73.2 - - - +
748u LYS* 1.3 60.2 + - - +
750u ILE* 4.0 4.8 - - - +
751u GLY* 2.9 27.0 + - - -
787u ILE* 6.3 1.3 - - + -
791u VAL* 4.9 13.0 - - + +
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Residues in contact with LYS 748 (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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707u LEU* 6.4 0.9 - - - -
710u ALA* 4.1 12.0 - - + +
744u ALA 2.9 17.7 + - - +
745u ALA* 3.6 8.5 - - - +
747u LEU* 1.3 75.5 - - - +
749u ALA* 1.3 57.7 + - - +
751u GLY* 3.8 0.8 - - - -
752u TYR* 2.9 31.2 + - - +
787u ILE* 5.0 15.8 - - + +
791u VAL* 5.9 2.0 - - - -
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Residues in contact with ALA 749 (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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706u ALA* 3.5 26.0 - - + +
709u ILE* 4.4 9.9 - - + +
710u ALA* 3.8 15.5 - - - +
713u ALA* 4.8 2.3 - - - +
731u LEU* 5.7 5.8 - - + -
745u ALA 3.0 13.1 + - - +
746u PHE* 3.6 8.3 - - - +
747u LEU 3.3 0.2 - - - -
748u LYS* 1.3 76.6 - - - +
750u ILE* 1.3 55.7 + - - +
752u TYR* 3.4 2.4 + - - +
753u LEU* 2.9 30.0 + - - +
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Residues in contact with ILE 750 (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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731u LEU* 5.4 10.2 - - + +
746u PHE 2.9 16.8 + - - +
747u LEU* 4.1 4.7 - - - +
749u ALA* 1.3 77.1 - - - +
751u GLY* 1.3 58.2 + - - +
753u LEU* 3.1 6.0 + - - +
754u ILE* 2.9 32.7 + - - +
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Residues in contact with GLY 751 (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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747u LEU 2.9 18.0 + - - -
748u LYS* 3.8 1.6 - - - -
750u ILE* 1.3 76.7 - - - +
752u TYR* 1.3 58.0 + - - +
754u ILE* 4.2 8.4 + - - +
755u PRO* 4.6 5.0 - - - +
791u VAL* 5.2 15.7 - - - -
794u GLN* 3.9 24.9 - - - +
795u CYS* 5.7 6.5 - - - -
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Residues in contact with TYR 752 (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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710u ALA* 3.9 15.7 - - + +
713u ALA* 3.5 30.6 - - + +
714u GLU* 4.5 7.9 - - + +
748u LYS 2.9 18.1 + - - +
749u ALA 3.9 2.0 - - - +
750u ILE 3.2 0.2 - - - -
751u GLY* 1.3 78.4 - - - +
753u LEU* 1.3 61.6 + - - +
755u PRO* 4.3 8.6 - - - +
756u LEU* 4.8 3.8 + - - +
794u GLN* 5.8 0.4 - - - -
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Residues in contact with LEU 753 (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 ALA* 3.9 11.0 - - + +
724u PHE* 5.8 8.3 - - + -
749u ALA 2.9 17.1 + - - +
750u ILE* 3.1 7.5 + - - +
752u TYR* 1.3 77.9 - - - +
754u ILE* 1.3 59.9 + - - +
755u PRO 3.4 0.2 - - - -
756u LEU* 3.0 29.2 + - - +
757u MET* 4.0 4.5 + - - +
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Residues in contact with ILE 754 (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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750u ILE 2.9 15.9 + - - +
751u GLY* 4.2 6.2 + - - +
752u TYR 3.5 0.6 - - - -
753u LEU* 1.3 76.7 - - - +
755u PRO* 1.3 59.6 - - - +
756u LEU 3.4 0.2 + - - -
757u MET* 3.5 15.2 + - - +
762u ALA* 3.6 31.6 - - + +
765u TYR* 5.3 9.6 - - + -
766u THR* 6.1 2.5 - - - +
794u GLN 5.7 2.9 - - - +
795u CYS* 6.1 4.5 - - + -
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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