Contacts of the strand formed by residues 262 - 269 (chain A) 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 ARG 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A LEU* 5.1 5.4 - - - +
144A VAL* 3.5 37.8 - - + +
145A GLY* 4.9 3.6 - - - +
159A SER* 3.5 0.9 - - - -
160A VAL* 3.0 49.6 + - + +
162A ASP* 2.8 40.9 + - - +
193A PRO* 4.0 22.0 - - - +
194A LEU* 3.9 17.3 - - - +
220A LEU* 5.0 1.8 - - - +
237A PRO* 3.4 22.6 - - - +
260A ASN 4.6 5.2 - - - +
261A PRO* 1.3 75.5 - - - +
263A ASP* 1.3 64.7 + - - +
264A ILE* 3.9 0.6 - - - +
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Residues in contact with ASP 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A VAL* 3.2 5.4 - - - +
145A GLY* 2.7 34.3 + - - +
146A PRO* 6.0 0.6 - - + +
156A LYS* 3.8 26.1 + - + +
158A GLY 3.6 5.6 - - - +
159A SER* 3.2 20.3 - - - -
261A PRO* 5.0 5.7 - - - +
262A ARG* 1.3 76.8 + - - +
264A ILE* 1.3 61.4 + - - +
265A TYR* 3.6 33.6 + - + +
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Residues in contact with ILE 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A PRO* 5.0 5.8 - - + -
101A LEU* 4.4 6.7 - - + -
105A MET* 3.9 25.8 - - + -
106A MET* 4.6 13.5 - - + -
142A PHE* 4.8 3.1 - - + -
143A ARG 3.2 13.0 - - - +
144A VAL* 4.1 16.8 - - + -
156A LYS* 3.5 4.9 - - - +
157A ILE* 2.9 42.5 + - + -
158A GLY* 2.8 15.6 + - - +
159A SER* 3.7 25.6 - - - -
160A VAL* 3.9 9.4 - - + +
262A ARG 3.9 4.7 - - - +
263A ASP* 1.3 80.3 - - - +
265A TYR* 1.3 69.1 + - - +
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Residues in contact with TYR 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ILE 4.4 0.2 - - - -
142A PHE* 3.2 9.9 - - - +
143A ARG* 2.8 32.9 + - + +
145A GLY 3.5 17.9 - - - -
146A PRO* 3.7 40.4 - - + +
147A GLN 6.1 0.2 - - - -
154A ALA* 4.2 18.2 - - + -
155A ARG 3.2 6.7 - - - +
156A LYS* 3.8 28.1 - - + +
157A ILE* 4.5 2.7 - - - -
263A ASP* 3.6 36.0 + - + -
264A ILE* 1.3 79.7 - - - +
266A MET* 1.3 59.2 + - - +
267A LEU* 3.8 19.3 - - + -
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Residues in contact with MET 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 3.6 22.2 - - + -
141A ILE 3.5 2.9 - - - -
142A PHE* 3.8 20.2 - - + -
153A ILE 3.4 4.9 - - - +
154A ALA* 3.4 0.9 - - - -
155A ARG* 2.7 54.9 + - + +
157A ILE* 4.2 7.8 - - + +
265A TYR* 1.3 73.2 - - - +
267A LEU* 1.3 63.2 + - - +
268A TYR* 4.4 15.6 - - + -
281A PHE* 5.3 0.2 - - - -
282A ILE* 4.5 13.0 - - + +
285A VAL* 3.5 36.6 - - + -
286A ILE* 3.9 27.4 - - + -
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Residues in contact with LEU 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A VAL* 3.3 6.1 - - - +
141A ILE* 2.6 54.2 + - + +
143A ARG* 3.8 28.3 - - + -
147A GLN* 3.8 26.5 - - + +
152A LEU* 3.7 29.4 - - + -
153A ILE 3.2 3.8 - - - +
154A ALA* 3.7 27.6 - - + -
265A TYR* 3.8 15.5 - - + -
266A MET* 1.3 76.8 - - - +
268A TYR* 1.3 66.1 + - - +
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Residues in contact with TYR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ASP 3.9 17.3 - - - +
140A VAL* 4.8 1.1 - - + -
152A LEU* 3.4 7.7 - - - +
153A ILE* 2.8 70.9 + - + +
155A ARG* 5.4 5.5 + - + +
266A MET* 4.4 23.1 - - + -
267A LEU* 1.3 81.3 - - - +
269A ASN* 1.3 75.0 + - - +
274A LEU* 4.2 11.9 - - + -
282A ILE* 3.7 46.9 - - + +
286A ILE* 4.7 7.6 - - - +
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Residues in contact with ASN 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PRO* 5.6 6.6 - - - +
136A THR* 5.2 14.1 - - - +
138A TRP 5.9 2.6 + - - +
139A ASP 4.8 2.6 + - - -
151A SER* 3.6 24.7 + - - -
152A LEU* 3.9 8.8 - - + +
153A ILE* 3.9 0.6 - - - +
268A TYR* 1.3 89.4 - - - +
270A HIS* 1.3 87.1 + - - +
274A LEU* 4.1 20.8 - - + +
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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