Contacts of the strand formed by residues 67 - 74 (chain F) in PDB entry 6X0A
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 TYR 67 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22C ASN* 3.9 19.6 + - - +
23C ASP* 3.7 31.2 + - + +
16F ILE* 4.3 32.0 - - + +
31F PHE* 4.8 18.2 - + + -
63F THR* 3.6 5.5 - - - -
64F ILE* 3.0 39.8 + - + +
65F GLY 4.3 0.2 - - - +
66F ASN* 1.3 85.5 - - - +
68F LEU* 1.3 65.2 + - - +
83F ILE* 4.5 11.0 - - + -
84F VAL* 3.6 7.0 - - - +
85F HIS* 3.4 41.1 - + + +
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Residues in contact with LEU 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F ARG* 3.9 29.8 - - - +
55F ILE* 4.4 3.8 - - + -
61F ALA* 4.0 13.9 - - + -
62F LEU 3.7 0.7 - - - -
63F THR* 3.3 33.4 - - + -
67F TYR* 1.3 77.2 - - - +
69F ILE* 1.3 62.6 + - - +
70F LEU* 3.7 25.5 + - + +
83F ILE* 3.2 26.4 - - - +
84F VAL* 2.8 16.7 + - + +
85F HIS 5.0 1.3 - - - +
86F GLY* 4.0 22.9 - - - -
87F ALA 4.8 2.5 - - - +
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Residues in contact with ILE 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F ILE* 4.0 22.4 - - + +
38F ARG* 4.6 5.4 - - + -
39F ILE* 3.2 46.2 - - + -
61F ALA* 3.4 4.0 - - - -
62F LEU* 2.7 56.5 + - + +
64F ILE* 4.2 20.6 - - + -
68F LEU* 1.3 75.2 - - - +
70F LEU* 1.3 61.5 + - - +
71F TYR* 3.5 7.0 + - + -
80F ILE* 4.1 20.4 - - + -
82F ARG 3.8 3.6 - - - +
83F ILE* 4.3 13.9 - - + -
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Residues in contact with LEU 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55F ILE* 3.6 46.7 - - + -
59F ALA* 5.4 5.2 - - + -
60F ARG 3.2 11.9 - - - +
61F ALA* 3.9 13.0 - - + -
68F LEU* 3.7 16.5 - - + +
69F ILE* 1.3 72.0 - - - +
71F TYR* 1.3 60.3 + - - +
80F ILE* 3.9 2.3 - - - +
81F VAL* 3.0 28.3 + - + -
82F ARG* 2.9 37.4 + - + +
84F VAL* 4.7 14.4 - - + +
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Residues in contact with TYR 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42F LEU* 3.6 27.7 - - + +
46F PRO 2.8 29.4 + - - -
49F GLY* 3.0 33.0 + - - -
59F ALA* 3.6 4.2 - - - +
60F ARG* 2.7 72.8 + - + +
61F ALA 3.8 6.5 - - - -
62F LEU* 4.2 2.7 - - + -
69F ILE* 3.5 13.9 - - + +
70F LEU* 1.3 75.1 - - - +
72F ARG* 1.3 66.5 + - - +
73F LEU* 4.3 8.3 - - + -
78F ILE* 3.8 18.2 - - + -
79F GLU 3.3 13.9 - - - +
80F ILE* 3.7 15.5 - - + -
81F VAL* 4.2 5.2 - - - +
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Residues in contact with ARG 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F ASP* 3.1 50.4 + - + +
59F ALA* 5.4 0.9 - - - -
60F ARG* 5.4 1.3 - - - -
71F TYR* 1.3 76.5 - - - +
73F LEU* 1.3 77.5 + - - +
74F ALA* 4.1 5.8 - - - +
78F ILE* 3.9 6.1 - - - +
79F GLU* 2.6 75.0 + - + +
81F VAL* 4.6 10.2 - - + +
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Residues in contact with LEU 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46F PRO* 3.4 50.3 - - + +
47F GLU* 4.4 8.5 - - + +
58F ASP* 4.8 2.4 + - - +
60F ARG* 3.8 21.6 - - - +
71F TYR* 4.3 11.0 - - + -
72F ARG* 1.3 89.4 + - - +
74F ALA* 1.3 63.2 + - - +
77F TRP 4.3 1.1 - - - +
78F ILE* 3.8 24.5 - - + -
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Residues in contact with ALA 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F ARG* 4.1 7.7 + - - +
73F LEU* 1.3 77.6 - - - +
75F GLU* 1.3 67.0 + - + +
76F GLY 3.0 4.7 + - - -
77F TRP* 3.0 55.0 + - + +
79F GLU* 3.4 13.9 - - - +
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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