Contacts of the helix formed by residues 65 - 76 (chain 9) 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 65 (chain 9).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159 LYS* 5.7 11.7 - - + +
189 LEU* 4.9 17.6 - - + +
649 LYS* 1.3 79.4 - - - +
669 GLY* 1.3 58.6 + - - +
689 ARG* 3.3 5.8 + - - +
699 LYS* 2.9 31.8 + - - +
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Residues in contact with GLY 66 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649 LYS 3.3 3.2 - - - +
659 ASP* 1.3 77.4 - - - +
679 LEU* 1.3 62.5 + - - +
699 LYS* 3.6 7.1 - - - +
709 GLU* 3.0 23.0 + - - +
234p GLU* 5.3 11.4 - - - -
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Residues in contact with LEU 67 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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649 LYS* 3.0 18.3 + - - +
669 GLY* 1.3 75.4 - - - +
689 ARG* 1.3 63.1 + - - +
709 GLU* 2.9 18.2 + - - +
719 GLU* 3.0 14.8 + - - +
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Residues in contact with ARG 68 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119 TYR* 5.0 20.0 - - + +
149 GLU* 5.8 4.3 - - + -
159 LYS* 5.6 9.0 - - + +
649 LYS 2.9 15.2 + - - +
659 ASP* 3.8 9.4 - - - +
679 LEU* 1.3 72.9 - - - +
699 LYS* 1.3 64.5 + - - +
719 GLU* 3.3 5.9 + - - +
729 LEU* 2.9 26.6 + - - +
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Residues in contact with LYS 69 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159 LYS* 6.2 1.0 - - - +
659 ASP 2.9 17.8 + - - +
669 GLY* 3.6 9.0 - - - +
689 ARG* 1.3 75.0 - - - +
709 GLU* 1.3 57.5 + - - +
729 LEU* 3.6 6.3 - - - +
739 ASN* 3.0 28.9 + - - +
232p GLU* 6.4 1.8 - - + -
234p GLU* 5.5 9.6 - - + -
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Residues in contact with GLU 70 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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669 GLY 3.0 13.4 + - - +
679 LEU* 2.9 14.3 + - - +
699 LYS* 1.3 72.8 - - - +
719 GLU* 1.3 66.8 + - - +
739 ASN* 2.9 18.8 + - - +
749 ALA* 3.0 13.0 + - - +
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Residues in contact with GLU 71 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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679 LEU 3.0 16.3 + - - +
689 ARG* 4.0 5.8 - - - +
709 GLU* 1.3 71.7 - - - +
729 LEU* 1.3 57.5 + - - +
749 ALA* 3.0 11.2 + - - +
759 ILE* 2.9 28.9 + - - +
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Residues in contact with LEU 72 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89 GLN* 5.9 6.9 - - + +
119 TYR* 4.5 19.0 - - + +
689 ARG 2.9 19.1 + - - +
699 LYS* 3.6 7.6 - - - +
719 GLU* 1.3 78.0 - - - +
739 ASN* 1.3 57.9 + - - +
759 ILE* 3.0 5.9 + - - +
769 SER* 2.9 34.4 + - - -
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Residues in contact with ASN 73 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699 LYS 3.0 14.2 + - - +
709 GLU* 2.9 11.7 + - - +
729 LEU* 1.3 76.2 - - - +
749 ALA* 1.3 59.3 + - - +
759 ILE 3.5 0.2 + - - -
769 SER* 3.9 14.4 + - - +
225p LEU* 5.2 11.6 - - - +
228p LYS* 5.3 8.7 - - + +
229p LEU* 4.8 23.8 - - + +
232p GLU* 5.2 9.4 - - + -
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Residues in contact with ALA 74 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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709 GLU 3.0 10.8 + - - +
719 GLU* 3.4 12.3 - - - +
739 ASN* 1.3 77.7 - - - +
759 ILE* 1.3 58.7 + - - +
769 SER 5.2 0.6 - - - -
225p LEU* 6.2 1.8 - - - -
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Residues in contact with ILE 75 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49 ILE* 5.3 14.2 - - + +
79 GLN* 6.2 3.6 - - + -
89 GLN* 5.9 8.5 - - + +
719 GLU 2.9 14.2 + - - +
729 LEU* 3.0 6.7 + - - +
749 ALA* 1.3 79.8 - - - +
769 SER* 1.3 63.6 + - - +
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Residues in contact with SER 76 (chain 9).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89 GLN* 5.7 7.6 - - - -
729 LEU* 2.9 16.8 + - - -
739 ASN* 3.9 12.1 + - - -
749 ALA 3.7 0.6 - - - -
759 ILE* 1.3 80.6 - - - +
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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