Contacts of the strand formed by residues 66 - 75 (chain D) in PDB entry 1FSK
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 66 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55D LYS* 4.0 37.7 - - + +
56D ILE 3.1 14.4 - - - +
57D SER* 4.5 2.7 - - - +
58D PHE* 4.0 7.1 - - - -
64D PHE* 3.7 2.0 - - - +
65D LYS* 1.3 97.7 - - + +
67D VAL* 1.3 78.2 + - - +
68D LYS* 3.7 25.6 - - + -
87D GLU* 3.0 21.2 + - - +
88D GLY* 3.7 36.1 + - - -
89D GLY* 3.7 5.6 + - - -
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Residues in contact with VAL 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54D LYS 3.6 0.5 - - - +
55D LYS* 3.7 0.2 - - - -
56D ILE* 2.8 52.8 + - + +
58D PHE* 3.8 19.5 - - + -
66D TYR* 1.3 82.0 - - - +
68D LYS* 1.3 65.5 + - - +
69D ASP* 3.7 11.0 - - - +
85D VAL* 3.3 28.3 - - + -
87D GLU 3.3 5.8 - - - -
88D GLY 3.3 18.2 - - - +
89D GLY* 5.2 1.6 - - - -
90D PRO* 4.7 5.6 - - + -
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Residues in contact with LYS 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D ILE* 4.7 18.5 - - + +
53D ILE* 4.8 8.3 - - + -
54D LYS 3.0 13.2 - - - +
55D LYS* 4.0 26.0 - - + +
66D TYR* 3.7 23.7 - - + -
67D VAL* 1.3 75.3 - - - +
69D ASP* 1.3 61.8 + - - +
85D VAL* 3.6 0.5 - - - +
86D ILE* 2.7 42.3 + - + +
87D GLU* 2.9 48.5 + - + +
31F SER* 5.2 8.0 + - - -
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Residues in contact with ASP 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D ILE* 3.7 5.9 - - - +
54D LYS* 3.1 33.5 + - + +
56D ILE* 3.7 24.8 - - + +
67D VAL* 3.7 20.6 - - - +
68D LYS* 1.3 81.9 - - - +
70D ARG* 1.3 64.2 + - - +
71D VAL 4.3 0.4 - - - -
83D TYR* 3.3 33.6 - - + -
84D SER 2.9 12.1 - - - +
85D VAL* 3.9 8.7 - - - +
86D ILE* 4.4 1.9 - - - +
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Residues in contact with ARG 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51D GLY 4.5 1.1 - - - +
52D THR 3.6 5.2 - - - -
53D ILE* 4.0 19.3 - - + -
69D ASP* 1.3 78.7 - - - +
71D VAL* 1.3 71.4 + - - +
72D ASP* 2.6 31.9 + - - +
83D TYR* 3.3 3.3 - - - -
84D SER* 2.9 27.3 + - - +
86D ILE* 3.9 30.0 - - + +
97D LYS* 3.8 14.3 - - - +
33F TRP* 4.7 12.7 - - + +
52F PHE* 4.0 16.6 - - - -
54F SER* 4.9 1.0 + - - -
55F ASP* 2.9 37.5 + - - +
57F TYR* 2.9 36.3 - - - -
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Residues in contact with VAL 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D GLY 4.9 3.1 - - - +
49D GLY 4.1 3.8 - - - +
50D PRO* 4.0 12.8 - - + -
51D GLY* 3.0 30.5 + - - +
52D THR* 3.0 21.9 + - - +
54D LYS* 4.0 26.9 - - + +
69D ASP* 4.3 0.8 - - - +
70D ARG* 1.3 74.4 - - - +
72D ASP* 1.3 61.4 + - - +
73D GLU 4.4 0.4 - - - +
74D VAL* 3.5 31.6 - - + -
81D TYR* 4.0 21.5 - - + +
82D ASN 4.0 4.5 - - - +
83D TYR* 4.1 4.2 - - - +
33F TRP* 5.5 0.7 - - - -
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Residues in contact with ASP 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D PRO* 5.4 0.4 - - - -
51D GLY* 5.0 0.9 - - - -
70D ARG* 2.6 35.5 + - - +
71D VAL* 1.3 73.2 - - - +
73D GLU* 1.3 66.8 + - + +
82D ASN* 3.0 19.9 + - + +
83D TYR 3.1 14.6 + - - -
84D SER* 2.3 29.1 + - - -
94E TYR* 3.9 21.2 - - - -
33F TRP* 5.4 2.0 - - - -
57F TYR* 3.7 35.6 + - + +
59F ASN* 4.9 1.2 + - - -
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Residues in contact with GLU 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D PRO* 5.3 4.3 - - - -
71D VAL* 3.9 0.6 - - - +
72D ASP* 1.3 81.9 - - + +
74D VAL* 1.3 79.8 + - - +
75D ASP* 3.6 29.2 + - - +
80D LYS* 4.1 11.1 - - - +
81D TYR* 3.6 0.5 - - - -
82D ASN* 2.9 54.1 + - + +
94E TYR* 5.6 3.8 - - + -
57F TYR* 5.1 3.8 - - - +
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Residues in contact with VAL 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE* 4.5 6.7 - - + -
24D LEU* 4.4 13.2 - - + -
49D GLY 5.7 0.4 - - - -
50D PRO* 4.6 20.8 - - + +
71D VAL* 3.5 25.6 - - + -
73D GLU* 1.3 89.9 - - - +
75D ASP* 1.3 62.6 + - - +
76D HIS* 3.4 42.0 + - + +
80D LYS 3.7 3.4 - - - +
81D TYR* 3.7 13.9 - - + +
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Residues in contact with ASP 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19D PHE* 3.8 3.6 - - - -
73D GLU* 3.6 16.7 + - - +
74D VAL* 1.3 71.7 - - - +
76D HIS* 1.3 63.8 + - - +
77D THR* 2.9 13.7 + - - -
78D ASN* 2.7 43.6 + - - +
79D PHE* 3.2 15.4 + - - -
80D LYS* 2.8 36.0 + - + +
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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