Contacts of the helix formed by residues 60 - 71 (chain x) 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 SER 60 (chain x).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288v VAL* 5.2 8.5 - - - -
306v GLU* 3.8 36.1 + - - +
335v VAL* 5.6 6.7 - - - -
54x ALA* 4.7 5.0 - - - +
58x ASN 4.0 0.4 + - - -
59x GLU* 1.3 79.7 - - - +
61x LYS* 1.3 65.9 + - - +
62x ALA* 3.5 6.5 - - - -
63x ARG* 4.1 8.3 - - - +
64x VAL* 3.5 19.8 + - - +
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Residues in contact with LYS 61 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337v ALA* 5.2 11.2 - - + -
352v GLU* 4.8 19.6 - - + +
50x LEU* 6.0 7.1 - - + +
54x ALA* 5.2 8.4 - - + +
60x SER* 1.3 74.9 - - - +
62x ALA* 1.3 61.0 + - - +
64x VAL* 3.2 6.9 + - - +
65x ARG* 2.9 27.5 + - - +
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Residues in contact with ALA 62 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233v ASN* 5.4 5.4 - - + +
286v ILE* 6.4 1.3 - - + -
287v PHE 3.8 22.2 - - - +
288v VAL* 4.2 19.2 - - + +
60x SER* 3.5 2.7 - - - -
61x LYS* 1.3 76.8 - - - +
63x ARG* 1.3 60.8 + - - +
65x ARG* 3.6 8.4 - - - +
66x PHE* 2.9 31.0 + - - +
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Residues in contact with ARG 63 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286v ILE* 6.2 5.2 - - + -
306v GLU* 5.4 6.7 - - + -
59x GLU* 4.1 17.0 - - + -
60x SER* 3.8 18.6 + - - +
62x ALA* 1.3 78.1 - - - +
64x VAL* 1.3 57.6 + - - +
66x PHE* 3.4 4.5 + - - +
67x ASN* 2.9 29.8 + - - +
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Residues in contact with VAL 64 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50x LEU* 5.6 5.6 - - + +
53x PHE* 5.6 11.0 - - + +
54x ALA* 5.4 9.2 - - + -
59x GLU* 5.0 5.7 - - + +
60x SER 3.5 11.0 + - - +
61x LYS* 3.2 10.1 + - - +
63x ARG* 1.3 74.8 - - - +
65x ARG* 1.3 59.4 + - - +
67x ASN* 3.9 5.4 - - - +
68x LEU* 2.9 33.4 + - - +
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Residues in contact with ARG 65 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44x MET* 5.8 10.7 - - + +
61x LYS 2.9 16.5 + - - +
62x ALA* 3.6 9.9 - - - +
64x VAL* 1.3 77.5 - - - +
66x PHE* 1.3 56.6 + - - +
68x LEU* 3.8 3.2 - - - +
69x MET* 2.9 30.5 + - - +
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Residues in contact with PHE 66 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233v ASN* 4.2 23.6 - - + -
62x ALA 2.9 17.2 + - - +
63x ARG* 4.0 4.5 - - - +
65x ARG* 1.3 74.3 - - - +
67x ASN* 1.3 60.7 + - - +
69x MET* 3.6 6.9 - - - +
70x GLU* 2.9 30.5 + - - +
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Residues in contact with ASN 67 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63x ARG 2.9 18.7 + - - +
64x VAL* 3.9 6.3 - - - +
66x PHE* 1.3 76.2 - - - +
68x LEU* 1.3 58.1 + - - +
70x GLU* 3.3 4.3 + - - +
71x LYS* 2.9 29.7 + - - +
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Residues in contact with LEU 68 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40x TYR* 4.1 26.6 - - + +
43x TYR* 5.7 6.7 - - + -
44x MET* 6.0 4.9 - - + -
64x VAL 2.9 18.7 + - - +
65x ARG* 4.2 3.1 - - - +
67x ASN* 1.3 76.1 - - - +
69x MET* 1.3 60.1 + - - +
71x LYS* 3.9 7.9 - - - +
72x MET* 3.6 13.3 + - - +
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Residues in contact with MET 69 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168v TYR* 6.1 7.0 - - + -
65x ARG 2.9 19.6 + - - +
66x PHE* 3.6 9.2 - - - +
67x ASN 3.1 0.2 - - - -
68x LEU* 1.3 77.2 - - - +
70x GLU* 1.3 60.5 + - - +
71x LYS 3.2 0.2 - - - -
72x MET* 3.2 23.3 + - - +
73x LEU 4.4 1.2 + - - -
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Residues in contact with GLU 70 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66x PHE 2.9 17.1 + - - +
67x ASN* 4.2 3.6 - - - +
69x MET* 1.3 76.3 - - - +
71x LYS* 1.3 59.5 + - - +
72x MET 3.2 0.4 - - - -
73x LEU* 3.4 19.0 + - - +
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Residues in contact with LYS 71 (chain x).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67x ASN 2.9 17.7 + - - +
68x LEU* 4.2 9.0 - - - +
69x MET 3.2 0.2 - - - -
70x GLU* 1.3 75.7 - - - +
72x MET* 1.3 62.5 + - - +
73x LEU 3.3 4.9 - - - -
74x GLN 5.0 2.0 - - - +
75x PRO* 3.3 32.0 - - + +
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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