Contacts of the helix formed by residues 65 - 75 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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64Y ASP* 1.3 74.3 - - - +
66Y VAL* 1.3 62.8 + - - +
67Y VAL 3.4 2.0 - - - -
68Y ILE* 4.1 9.4 - - - +
69Y GLU* 3.5 20.4 + - - +
650u ALA 5.1 0.3 - - - +
654u SER* 4.2 25.3 - - - -
655u LYS 5.7 1.6 - - - +
656u LYS* 6.2 4.3 - - + -
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Residues in contact with VAL 66 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64Y ASP* 4.3 3.4 - - + +
65Y ASP* 1.3 78.7 - - - +
67Y VAL* 1.3 58.4 + - - +
69Y GLU* 3.5 1.8 + - - -
70Y PHE* 2.9 23.9 + - - +
650u ALA* 3.7 25.4 - - + +
651u VAL* 5.5 5.8 - - + +
654u SER* 5.5 2.2 - - - -
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Residues in contact with VAL 67 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56Y VAL* 5.7 9.2 - - + -
64Y ASP* 4.8 11.7 - - + +
65Y ASP 3.4 1.2 - - - +
66Y VAL* 1.3 78.4 - - - +
68Y ILE* 1.3 58.3 + - - +
70Y PHE* 3.2 9.9 + - + +
71Y ILE* 3.0 27.7 + - - +
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Residues in contact with ILE 68 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49Y LYS 6.1 0.9 - - - +
52Y ILE* 6.5 0.9 - - - -
53Y THR* 5.7 12.8 - - - +
64Y ASP 4.8 5.3 + - - +
65Y ASP* 4.0 15.5 + - - +
67Y VAL* 1.3 78.3 - - - +
69Y GLU* 1.3 56.2 + - - +
71Y ILE* 3.4 7.0 + - - +
72Y PHE* 2.9 26.6 + - - +
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Residues in contact with GLU 69 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65Y ASP 3.5 15.9 + - - +
66Y VAL 3.7 0.2 - - - -
67Y VAL 3.3 0.2 - - - -
68Y ILE* 1.3 75.6 - - - +
70Y PHE* 1.3 59.5 + - - +
72Y PHE* 3.5 10.1 - - + +
73Y ASN* 2.9 31.7 + - - +
649u LYS 5.1 1.6 - - - +
650u ALA* 3.7 34.5 - - + +
653u LYS* 6.5 1.3 - - + -
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Residues in contact with PHE 70 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66Y VAL 2.9 15.4 + - - +
67Y VAL* 3.2 15.6 + - + +
69Y GLU* 1.3 75.5 - - - +
71Y ILE* 1.3 57.7 + - - +
73Y ASN* 3.4 2.9 + - - +
74Y GLN* 2.9 33.1 + - - +
646u PRO* 5.3 6.4 - - - +
650u ALA* 4.4 4.0 - - + +
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Residues in contact with ILE 71 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52Y ILE* 5.5 11.0 - - + -
67Y VAL 3.0 12.6 + - - +
68Y ILE* 3.8 9.2 - - - +
70Y PHE* 1.3 75.6 - - - +
72Y PHE* 1.3 56.3 + - - +
74Y GLN* 3.5 4.0 + - - +
75Y LEU* 2.9 33.3 + - - +
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Residues in contact with PHE 72 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68Y ILE 2.9 18.1 + - - +
69Y GLU* 3.5 12.6 - - + +
71Y ILE* 1.3 75.5 - - - +
73Y ASN* 1.3 57.0 + - - +
75Y LEU* 3.2 5.4 + - - +
76Y GLU* 2.9 25.6 + - - +
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Residues in contact with ASN 73 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69Y GLU 2.9 20.2 + - - +
70Y PHE 4.2 0.2 - - - +
72Y PHE* 1.3 74.2 - - - +
74Y GLN* 1.3 60.5 + - - +
76Y GLU* 3.4 19.9 + - - +
77Y VAL* 4.3 3.8 + - - +
646u PRO* 3.7 34.1 - - + +
649u LYS* 5.0 9.6 - - + -
650u ALA 5.8 0.2 - - - +
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Residues in contact with GLN 74 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70Y PHE 2.9 18.3 + - - +
71Y ILE* 4.2 4.0 - - - +
73Y ASN* 1.3 77.2 - - - +
75Y LEU* 1.3 58.8 + - - +
76Y GLU 3.4 0.2 - - - -
77Y VAL* 4.3 7.6 + - - +
80Y PRO* 3.5 25.3 - - + +
85Y MET* 5.8 8.3 - - + -
646u PRO* 5.1 4.0 - - + +
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Residues in contact with LEU 75 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40Y MET* 4.2 13.0 - - + +
45Y LEU* 6.6 0.2 - - + -
71Y ILE 2.9 19.0 + - - +
72Y PHE* 3.5 4.9 - - - +
74Y GLN* 1.3 76.3 - - - +
76Y GLU* 1.3 64.9 + - - +
77Y VAL 3.3 9.3 - - - +
80Y PRO* 5.3 1.8 - - - -
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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