Contacts of the strand formed by residues 257 - 268 (chain F) 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 TRP 257 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163F ILE* 4.5 2.6 - - - +
164F LEU* 5.1 8.9 + - + +
178F THR 5.3 1.6 + - - -
179F HIS* 4.0 22.2 - + - +
180F ALA* 3.7 20.0 - - + +
199F LEU* 3.7 24.7 - - + -
200F ILE 3.5 24.9 - - - -
201F ASN* 3.7 25.3 - - + +
205F GLU* 3.4 29.2 - - + -
207F VAL* 3.6 28.0 - - + -
252F ARG* 2.9 22.7 + - - -
253F ILE 4.9 0.5 - - - +
254F LEU* 2.9 45.0 + - + +
256F ASP* 1.3 92.9 + - + +
258F SER* 1.3 60.7 + - - +
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Residues in contact with SER 258 (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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161F LYS* 3.6 36.5 + - - +
162F ASP 3.4 15.3 - - - -
163F ILE* 4.2 3.6 - - - +
164F LEU* 6.5 0.2 - - - -
199F LEU* 3.6 7.7 - - - -
200F ILE* 3.0 41.2 + - - +
252F ARG* 4.4 1.1 - - - -
256F ASP 4.4 0.2 + - - -
257F TRP* 1.3 75.8 - - - +
259F ALA* 1.3 61.7 + - - +
261F PRO* 5.1 4.9 - - - +
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Residues in contact with ALA 259 (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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161F LYS* 3.8 1.0 - - - -
162F ASP* 2.9 46.9 + - + +
194F LEU* 5.9 0.9 - - + -
198F THR 3.2 24.2 - - - +
199F LEU* 4.2 3.4 - - + -
200F ILE* 5.1 1.1 - - - -
235F LEU* 4.0 18.6 - - + -
258F SER* 1.3 73.6 - - - +
260F ASN* 1.3 68.9 + - + +
261F PRO* 3.4 4.7 - - - -
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Residues in contact with ASN 260 (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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162F ASP* 4.2 6.9 + - - +
194F LEU* 6.1 1.6 - - + -
198F THR 4.7 1.8 + - - -
200F ILE* 5.5 1.0 - - - +
259F ALA* 1.3 72.1 - - + +
261F PRO* 1.3 76.3 - - - +
262F ARG* 2.7 59.9 + - - +
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Residues in contact with PRO 261 (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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160F VAL 3.4 7.6 - - - +
161F LYS* 3.9 22.0 - - + -
200F ILE* 5.1 12.1 - - + -
258F SER* 5.1 6.1 - - - +
259F ALA* 3.4 5.8 - - - +
260F ASN* 1.3 93.8 - - - +
262F ARG* 1.3 60.2 + - - +
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Residues in contact with ARG 262 (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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101F LEU* 4.6 7.9 - - - +
144F VAL* 3.4 34.7 - - + +
145F GLY* 5.1 2.5 - - - +
159F SER* 3.2 3.7 - - - -
160F VAL* 2.8 64.0 + - + +
161F LYS* 4.0 3.8 - - - +
162F ASP* 3.0 38.3 + - - -
237F PRO* 4.0 17.0 - - - +
260F ASN* 2.7 52.7 + - - +
261F PRO* 1.3 75.8 - - - +
263F ASP* 1.3 63.0 + - - +
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Residues in contact with ASP 263 (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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144F VAL* 3.6 4.7 - - - +
145F GLY* 2.9 29.1 + - - +
146F PRO* 6.2 0.4 - - + -
156F LYS* 3.1 35.2 + - + +
158F GLY 3.4 6.5 - - - +
159F SER* 3.1 21.8 - - - -
262F ARG* 1.3 78.1 - - - +
264F ILE* 1.3 62.9 + - - +
265F TYR* 3.8 25.3 + - + -
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Residues in contact with ILE 264 (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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98F PRO* 5.1 1.1 - - + -
101F LEU* 4.1 8.7 - - + -
105F MET* 3.7 30.5 - - + -
142F PHE* 5.2 4.7 - - + -
143F ARG 3.5 10.5 - - - +
144F VAL* 3.8 27.8 - - + -
156F LYS* 3.5 4.0 - - - +
157F ILE* 2.8 53.7 + - + +
158F GLY* 2.8 27.6 + - - +
159F SER* 4.4 0.4 - - - +
160F VAL* 4.0 23.8 - - + -
263F ASP* 1.3 81.2 - - - +
265F TYR* 1.3 63.2 + - - +
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Residues in contact with TYR 265 (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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141F ILE 3.5 1.0 - - - +
142F PHE* 3.3 5.7 - - - +
143F ARG* 2.9 36.2 + - + +
145F GLY 3.3 22.4 - - - +
146F PRO* 3.6 35.8 - - + +
154F ALA* 4.3 16.6 - - + -
155F ARG 3.2 4.9 - - - -
156F LYS* 3.7 34.3 - - + +
157F ILE* 4.5 4.0 - - - -
263F ASP* 3.8 33.5 + - + -
264F ILE* 1.3 77.6 - - - +
266F MET* 1.3 59.2 + - - +
267F LEU* 4.1 16.2 - - + -
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Residues in contact with MET 266 (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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140F VAL* 3.5 17.0 - - + -
141F ILE 3.4 3.6 - - - -
142F PHE* 3.8 25.6 - - + -
153F ILE 3.7 1.0 - - - +
154F ALA* 3.4 1.9 - - - -
155F ARG* 2.7 67.0 + - - +
157F ILE* 4.2 7.3 - - + +
265F TYR* 1.3 72.3 - - - +
267F LEU* 1.3 62.9 + - - +
268F TYR* 3.7 27.4 - - + -
281F PHE* 4.9 0.2 - - - -
282F ILE* 3.9 27.8 - - + +
285F VAL* 3.6 35.0 - - + -
286F ILE* 4.6 1.3 - - + -
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Residues in contact with LEU 267 (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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140F VAL* 3.4 8.8 - - - +
141F ILE* 2.8 58.6 + - + +
143F ARG* 3.7 27.6 - - + +
147F GLN* 4.0 30.5 - - + +
152F LEU* 4.2 20.0 - - + -
153F ILE 3.2 6.1 - - - +
154F ALA* 3.5 31.0 - - + -
265F TYR* 4.3 11.0 - - + -
266F MET* 1.3 75.9 - - - +
268F TYR* 1.3 62.0 + - - +
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Residues in contact with TYR 268 (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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139F ASP 4.1 13.9 - - - +
140F VAL* 4.6 0.2 - - + -
152F LEU* 3.4 12.8 - - - +
153F ILE* 2.8 70.6 + - + +
155F ARG* 4.5 12.9 + - + +
266F MET* 3.7 33.2 - - + +
267F LEU* 1.3 78.4 - - - +
269F ASN* 1.3 78.5 + - - +
274F LEU* 4.7 6.7 - - + -
278F VAL* 5.4 0.2 - - + -
279F ARG* 4.5 10.5 + - - -
282F ILE* 3.8 48.2 - - + +
286F ILE* 4.7 8.0 - - - +
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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