Contacts of the strand formed by residues 285 - 295 (chain B) in PDB entry 5F0P
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 285 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206B HIS* 5.6 1.2 - - - -
208B GLU* 4.8 11.7 + - - -
210B GLN* 5.0 4.9 - - - +
232B LYS* 5.1 7.9 - - - +
277B VAL* 3.7 20.1 - - + +
278B LEU 3.4 6.7 - - - +
279B VAL* 4.1 23.6 - - + +
283B ASP 3.1 18.8 + - - +
284B ARG* 1.3 73.9 - - - +
286B TYR* 1.3 63.3 + - - +
287B PHE* 4.6 0.8 - - - -
552D PRO* 3.7 30.0 - - - +
553D GLU 3.0 14.8 + - - +
554D LEU* 3.4 24.2 - - + +
555D TYR* 2.9 26.9 + - - +
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Residues in contact with TYR 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B ILE* 3.9 20.9 - - + -
174B LEU* 5.1 3.4 - - + -
202B ILE* 3.9 29.7 - - + +
276B LEU 3.9 0.2 - - - +
277B VAL* 3.4 2.1 - - - -
278B LEU* 2.8 54.9 + - + +
280B ASP* 3.2 23.2 + - + -
284B ARG* 3.7 29.1 - - + +
285B ARG* 1.3 71.8 - - - +
287B PHE* 1.3 60.0 + - - +
133C PRO* 3.5 35.6 - - + +
555D TYR* 3.4 38.1 - + + +
557D MSE 4.2 20.4 - - + -
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Residues in contact with PHE 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275B ASN* 3.4 22.4 - - - +
276B LEU 3.1 13.7 - - - +
277B VAL* 4.1 11.9 - - + -
285B ARG 4.6 1.3 - - - -
286B TYR* 1.3 75.4 - - - +
288B LYS* 1.3 65.1 + - - +
289B GLN* 4.9 12.8 - - + -
554D LEU* 3.9 32.5 - - + -
555D TYR 3.1 17.3 + - - -
556D LEU* 3.5 42.2 - - + +
557D MSE 2.9 31.4 + - - +
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Residues in contact with LYS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B MSE 4.2 21.8 - - - +
168B VAL* 4.1 27.6 - - + -
178B PHE* 4.1 17.6 - - + -
180B TYR* 5.3 0.5 + - - -
274B LEU 3.7 1.9 - - - +
275B ASN* 3.4 4.0 - - - +
276B LEU* 2.9 38.5 + - + +
287B PHE* 1.3 76.3 - - - +
289B GLN* 1.3 77.9 + - - +
290B GLN* 3.3 16.0 + - - +
556D LEU* 4.2 11.9 - - + -
557D MSE 3.6 24.1 - - + +
559D THR* 4.3 6.7 - - - -
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Residues in contact with GLN 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212B ILE* 4.0 17.8 - - - +
214B LYS* 3.3 34.6 + - - +
273B PHE* 3.6 30.8 - - + -
274B LEU 3.5 4.0 - - - +
275B ASN* 3.9 19.2 + - + +
287B PHE* 4.7 12.8 - - + -
288B LYS* 1.3 98.3 + - - +
290B GLN* 1.3 65.4 - - - +
556D LEU* 5.1 2.7 - - + +
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Residues in contact with GLN 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ILE* 3.6 30.8 - - + +
166B MSE 3.5 14.2 - - - +
178B PHE* 3.7 28.7 - - + -
180B TYR* 4.3 12.1 - - + -
273B PHE* 3.3 3.8 - - - -
274B LEU* 2.7 43.5 + - + +
288B LYS* 3.3 22.0 + - - +
289B GLN* 1.3 76.0 - - - +
291B GLU* 1.3 66.7 + - - +
292B ILE* 4.3 0.7 - - + +
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Residues in contact with GLU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ILE* 3.8 12.6 - - - +
183B SER* 4.7 1.2 - - - +
260B THR* 4.6 9.2 - - - +
262B ARG* 4.9 2.6 + - - -
271B ARG* 2.9 49.4 + - - +
272B TYR 3.2 20.2 - - - +
273B PHE* 3.7 24.2 - - + -
290B GLN* 1.3 78.3 + - - +
292B ILE* 1.3 69.7 + - - +
293B ILE* 4.5 17.5 - - + +
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Residues in contact with ILE 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B ILE* 4.1 13.2 - - + -
180B TYR* 5.4 0.2 - - + -
183B SER 3.4 13.9 - - - +
185B TYR* 4.1 14.8 - - + -
191B ILE* 4.1 15.5 - - + -
211B LEU* 4.1 12.8 - - + -
252B LEU* 5.2 1.6 - - + -
260B THR* 3.6 6.6 + - - -
272B TYR* 3.0 28.0 + - + +
273B PHE 4.7 0.9 - - - +
274B LEU* 3.8 41.7 - - + +
290B GLN* 4.3 2.5 - - + +
291B GLU* 1.3 83.3 - - - +
293B ILE* 1.3 64.4 + - - +
294B LEU* 3.5 26.4 + - + -
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Residues in contact with ILE 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183B SER* 3.1 16.1 + - - +
184B LYS* 3.3 22.6 - - + +
185B TYR 2.9 26.2 + - - +
260B THR* 3.5 21.1 - - + -
291B GLU* 4.5 17.3 - - + +
292B ILE* 1.3 76.6 - - - +
294B LEU* 1.3 75.3 - - - +
295B TRP* 4.8 2.0 - - + -
403B EDO 3.8 29.4 - - - +
409B EDO 6.3 0.7 - - - -
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Residues in contact with LEU 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185B TYR* 3.2 21.8 - - + +
186B HIS 5.1 0.4 - - - +
187B LEU* 4.2 7.6 - - + -
211B LEU* 5.0 5.8 - - + -
252B LEU* 4.1 11.0 - - + -
257B PRO* 3.8 29.2 - - + -
258B THR 3.8 13.2 - - - +
259B PRO* 3.9 1.5 - - - +
260B THR* 3.0 30.1 + - - +
272B TYR* 3.6 37.9 - - + -
292B ILE* 3.5 27.3 + - + -
293B ILE* 1.3 83.2 - - - +
295B TRP* 1.3 63.1 + - - +
409B EDO 4.3 1.6 - - - -
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Residues in contact with TRP 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ALA* 3.7 13.0 - - + -
156B THR 3.6 21.1 - - - -
157B TYR* 3.8 27.8 - + - -
158B PRO* 3.9 14.7 - - + +
161B ASN* 5.8 0.7 - - - -
182B LYS* 6.1 1.6 - - - -
184B LYS* 3.7 25.7 + - + +
185B TYR 3.1 28.3 + - - -
186B HIS* 3.1 39.7 - + + +
187B LEU* 3.2 13.2 + - - +
259B PRO* 4.4 1.3 - - - -
293B ILE* 4.1 1.6 - - + -
294B LEU* 1.3 77.1 - - - +
296B ARG* 1.3 77.6 + - - +
297B LYS* 3.5 37.0 - - + -
403B EDO 3.9 27.8 + - - -
409B EDO 3.8 16.8 - - - +
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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