Contacts of the strand formed by residues 259 - 269 (chain D) in PDB entry 5FHK
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 ALA 259 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161D LYS* 3.8 1.2 - - - -
162D ASP* 2.8 46.1 + - + +
194D LEU* 5.7 1.3 - - + -
198D THR 3.4 24.2 - - - +
199D LEU* 4.3 2.9 - - + -
200D ILE* 4.9 0.9 - - - -
235D LEU* 4.1 18.6 - - + -
258D SER* 1.3 74.4 - - - +
260D ASN* 1.3 71.0 + - + +
261D PRO* 3.4 4.7 - - - -
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Residues in contact with ASN 260 (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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162D ASP* 4.0 8.1 + - - +
194D LEU* 5.8 3.6 - - + +
198D THR 4.5 2.8 + - - -
200D ILE* 5.4 0.8 - - - +
259D ALA* 1.3 74.5 - - + +
261D PRO* 1.3 82.3 - - - +
262D ARG* 2.8 53.3 + - - +
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Residues in contact with PRO 261 (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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160D VAL 3.6 8.1 - - - +
161D LYS* 4.0 14.8 - - + -
200D ILE* 5.0 13.7 - - + -
258D SER* 5.4 3.4 - - - +
259D ALA* 3.4 3.7 - - - -
260D ASN* 1.3 94.7 - - - +
262D ARG* 1.3 61.3 + - - +
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Residues in contact with ARG 262 (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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101D LEU* 4.3 8.1 - - - +
144D VAL* 3.6 31.8 - - + +
145D GLY* 5.0 3.1 - - - +
159D SER* 3.3 4.5 - - - -
160D VAL* 2.9 57.4 + - + +
161D LYS* 4.0 3.8 - - - +
162D ASP* 3.0 42.4 + - - +
194D LEU* 5.8 0.2 - - - +
237D PRO* 3.6 21.6 - - - +
260D ASN* 2.8 52.0 + - - +
261D PRO* 1.3 74.1 - - - +
263D ASP* 1.3 65.8 + - - +
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Residues in contact with ASP 263 (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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144D VAL* 3.6 3.1 - - - +
145D GLY* 2.8 33.2 + - - +
146D PRO* 5.8 1.4 - - + +
156D LYS* 3.1 35.5 - - + +
158D GLY 3.5 2.9 - - - -
159D SER* 3.5 13.3 - - - -
262D ARG* 1.3 77.1 - - - +
264D ILE* 1.3 61.5 + - - +
265D TYR* 3.7 24.9 + - + -
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Residues in contact with ILE 264 (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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98D PRO* 5.0 3.8 - - + -
101D LEU* 3.8 27.4 - - + -
105D MET* 3.7 33.7 - - + -
106D MET* 5.0 1.3 - - + -
142D PHE* 5.1 3.1 - - + -
143D ARG 3.4 11.7 - - - +
144D VAL* 3.8 19.3 - - + -
156D LYS* 3.6 4.5 - - - +
157D ILE* 2.9 50.2 + - + +
158D GLY 2.8 23.7 + - - +
159D SER* 4.5 5.2 - - - +
160D VAL* 4.2 11.9 - - + -
263D ASP* 1.3 77.1 - - - +
265D TYR* 1.3 61.2 + - - +
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Residues in contact with TYR 265 (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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141D ILE 3.6 0.9 - - - +
142D PHE* 3.2 6.1 - - - +
143D ARG* 2.8 42.0 + - + +
145D GLY 3.5 17.5 - - - +
146D PRO* 3.8 33.5 - - + +
147D GLN* 5.7 0.9 - - - -
154D ALA* 4.2 18.2 - - + -
155D ARG 3.3 17.0 - - - -
156D LYS* 3.8 29.2 - - + +
157D ILE* 4.5 4.3 - - - -
263D ASP* 3.7 27.1 + - + -
264D ILE* 1.3 76.1 - - - +
266D MET* 1.3 58.2 + - - +
267D LEU* 4.0 15.9 - - + -
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Residues in contact with MET 266 (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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140D VAL* 3.6 22.0 - - + -
141D ILE 3.4 3.8 - - - -
142D PHE* 3.6 32.1 - - + -
153D ILE 3.5 4.5 - - - +
154D ALA* 3.5 0.9 - - - -
155D ARG* 2.9 59.8 + - + +
157D ILE* 4.1 8.4 - - + +
265D TYR* 1.3 71.0 - - - +
267D LEU* 1.3 65.0 + - - +
268D TYR* 4.7 8.8 - - + -
281D PHE* 4.9 0.7 - - - -
282D ILE* 4.5 21.5 - - + +
285D VAL* 3.8 31.9 - - + -
286D ILE* 4.4 8.3 - - + -
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Residues in contact with LEU 267 (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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140D VAL* 3.4 6.4 - - - +
141D ILE* 2.7 58.4 + - + +
143D ARG* 3.7 27.8 - - + -
147D GLN* 3.7 22.4 - - + +
152D LEU* 4.0 25.4 - - + -
153D ILE 3.3 4.0 - - - +
154D ALA* 3.6 29.2 - - + -
265D TYR* 4.0 15.0 - - + -
266D MET* 1.3 78.0 - - - +
268D TYR* 1.3 64.6 + - - +
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Residues in contact with TYR 268 (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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139D ASP 3.6 17.7 - - - +
140D VAL* 4.7 1.6 - - + -
152D LEU* 3.3 8.8 - - - -
153D ILE* 2.8 71.8 + - + +
155D ARG* 6.1 2.5 - - + -
266D MET* 4.7 15.0 - - + -
267D LEU* 1.3 77.4 - - - +
269D ASN* 1.3 68.7 + - - +
270D HIS* 5.4 0.9 - + - -
274D LEU* 3.5 30.7 - - + -
278D VAL* 5.3 0.4 - - + -
282D ILE* 3.5 41.8 - - + +
286D ILE* 6.1 0.7 - - + -
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Residues in contact with ASN 269 (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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135D PRO* 3.2 33.6 + - - +
136D THR* 4.0 14.8 + - - +
138D TRP 3.2 15.6 + - - -
139D ASP* 4.5 4.6 + - - +
151D SER* 4.5 6.4 + - - +
152D LEU* 3.4 22.0 - - - +
268D TYR* 1.3 86.2 - - - +
270D HIS* 1.3 60.6 + - - +
271D LYS* 2.8 36.2 + - + +
274D LEU* 3.7 8.9 - - + +
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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