Contacts of the strand formed by residues 83 - 90 (chain D) in PDB entry 6F8F
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 83 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74D LYS* 3.5 3.3 - - - -
75D GLY* 2.7 31.7 + - - -
79D GLU 4.2 9.6 - - - -
80D SER 2.6 19.5 + - - +
81D LYS 3.3 0.6 - - - -
82D ASP* 1.3 79.8 - - + +
84D LEU* 1.3 59.4 + - - +
134D LYS 4.2 2.9 - - - +
135D LYS* 3.7 62.4 - - + -
137D ILE 3.3 6.1 - - - +
138D ARG* 3.0 55.3 + - + -
139D ARG* 4.1 5.2 - - - -
223G PRO* 2.3 45.6 + - + +
224G GLU 3.7 9.0 - - - -
225G GLN* 4.7 1.3 - - - -
226G ASP 5.1 0.7 - - - -
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Residues in contact with LEU 84 (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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41D PHE* 3.7 35.7 - - + -
71D VAL* 3.9 20.0 - - + -
72D ASN 3.5 5.8 - - - +
73D PRO* 3.7 8.7 - - + +
83D TYR* 1.3 72.5 - - - +
85D SER* 1.3 75.0 + - - +
86D LEU* 4.1 5.4 - - + -
106D ILE* 6.4 0.2 - - + -
134D LYS 4.3 0.2 - - - -
136D PHE* 2.9 51.5 + - + +
137D ILE* 2.8 26.5 + - + +
139D ARG* 4.0 4.2 - - + +
142D LEU* 4.2 8.7 - - + -
155D LEU* 3.8 14.6 - - + -
157D LEU* 5.0 6.5 - - + -
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Residues in contact with SER 85 (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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71D VAL* 3.1 9.9 - - - +
72D ASN* 3.0 51.8 + - - +
75D GLY* 3.7 17.8 - - - -
76D LEU 4.9 0.5 + - - -
83D TYR 3.7 0.4 + - - -
84D LEU* 1.3 74.6 - - - +
86D LEU* 1.3 61.4 + - - +
87D TYR* 3.7 11.4 - - - -
133D PHE 3.4 9.2 - - - -
134D LYS* 2.5 31.2 + - - +
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Residues in contact with LEU 86 (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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69D LEU* 4.6 15.3 - - + -
70D ARG 3.6 3.8 - - - +
71D VAL* 3.5 24.5 - - + -
84D LEU* 4.1 4.3 - - + -
85D SER* 1.3 74.9 - - - +
87D TYR* 1.3 66.8 + - - +
104D PHE* 3.5 47.8 - - + -
132D GLY* 3.4 2.1 - - - -
133D PHE* 2.8 36.3 + - - +
136D PHE* 3.9 33.0 - - + +
157D LEU* 3.9 24.0 - - + -
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Residues in contact with TYR 87 (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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69D LEU* 3.3 9.5 - - - +
70D ARG* 2.9 88.3 + - + +
72D ASN* 3.8 1.1 - - - -
85D SER* 3.7 20.5 - - - -
86D LEU* 1.3 77.5 - - - +
88D LEU* 1.3 59.1 + - - +
104D PHE* 3.8 6.5 - - - -
130D ASP* 4.0 18.8 - - + -
131D TRP 3.5 7.2 - - - +
132D GLY* 3.3 26.0 - - - -
133D PHE 4.4 0.2 - - - -
134D LYS* 3.4 36.0 - - - +
230G THR* 3.7 21.4 + - - -
231G SER 5.0 0.5 + - - -
232G GLY* 4.3 10.6 - - - -
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Residues in contact with LEU 88 (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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57D PHE* 4.0 22.0 - - + -
67D TRP* 3.6 39.5 - - + -
68D CYS 3.8 9.6 - - - +
69D LEU* 4.1 6.7 - - + -
87D TYR* 1.3 71.0 - - - +
89D LEU* 1.3 60.6 + - - +
100D ALA* 5.3 0.4 - - + -
102D PHE* 4.0 17.3 - - + -
104D PHE* 3.6 16.4 - - + -
125D PHE* 3.4 18.8 - - + -
130D ASP* 3.1 3.1 - - - -
131D TRP 2.9 35.0 + - - +
159D CYS* 4.4 0.9 - - - -
161D VAL* 3.9 28.7 - - + -
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Residues in contact with LEU 89 (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 LYS* 3.6 34.3 - - + +
67D TRP* 3.2 9.2 - - - +
68D CYS* 2.8 56.7 + - - +
70D ARG* 5.1 9.4 - - + -
87D TYR 4.0 0.2 - - - -
88D LEU* 1.3 73.6 - - - +
90D LEU* 1.3 76.6 + - - +
91D VAL* 4.3 5.4 - - + -
128D GLY* 3.5 36.1 - - - +
129D LYS 3.5 6.3 - - - +
130D ASP* 3.8 14.6 - - + +
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Residues in contact with LEU 90 (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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65D LEU* 4.2 12.1 - - + -
66D LYS 3.8 13.2 - - - +
67D TRP* 3.8 34.4 - - + -
89D LEU* 1.3 73.6 - - - +
91D VAL* 1.3 59.3 + - - +
92D SER* 3.8 14.4 - - - +
94D PRO* 3.9 22.4 - - + -
98D VAL* 4.2 3.1 - - + -
125D PHE* 3.9 23.8 - - + +
126D VAL* 3.4 36.3 - - - +
127D GLN 3.7 3.8 - - - +
128D GLY 2.9 28.1 + - - -
129D LYS 3.1 7.9 + - - -
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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