Contacts of the helix formed by residues 291 - 300 (chain B) in PDB entry 5FQD
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 ASP 291 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B ILE* 1.3 75.7 - - - +
292B ASP* 1.3 60.0 + - - +
293B VAL* 3.2 23.2 - - - +
294B LEU* 3.3 32.3 + - - +
295B ARG* 3.0 24.4 + - - +
324B LYS* 3.5 26.7 - - - +
419B ARG* 3.7 4.5 - - - +
422B LEU 4.4 4.0 - - - +
423B LEU* 3.6 21.3 - - + +
424B PRO* 3.7 14.9 - - + +
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Residues in contact with ASP 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B MET 4.9 5.9 - - - +
90B ILE* 3.3 29.4 - - + +
125B TYR 4.9 5.9 - - - +
291B ASP* 1.3 71.7 - - - +
293B VAL* 1.3 59.7 + - - +
295B ARG* 4.3 1.1 - - - -
296B ILE* 2.9 38.7 + - + +
324B LYS* 3.4 18.0 + - - +
419B ARG* 3.4 26.9 + - - +
420B SER* 5.0 6.8 - - - -
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ASP* 3.2 25.8 - - + +
292B ASP* 1.3 77.2 - - - +
294B LEU* 1.3 66.6 + - + +
296B ILE* 3.6 7.9 + - - +
297B GLN* 3.2 38.6 + - + +
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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
----------------------------------------------------------
290B ILE* 3.7 32.9 - - + +
291B ASP* 3.3 26.0 + - - +
293B VAL* 1.3 81.0 - - + +
295B ARG* 1.3 58.4 + - - +
297B GLN* 3.2 10.2 + - + +
298B LEU* 2.9 27.4 + - - +
314B ILE* 4.8 9.9 - - + +
318B CYS* 5.1 0.7 - - - -
424B PRO* 4.1 8.1 - - + -
432B GLU* 3.7 36.3 - - + +
433B ILE* 5.9 0.2 - - - -
434B SER* 4.0 26.9 - - - +
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Residues in contact with ARG 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B ILE* 2.9 48.2 + - + -
92B ILE* 3.4 24.5 - - + +
95B GLN* 3.8 2.2 + - - -
285B ALA 3.8 10.1 + - - -
286B ALA 3.2 18.2 + - - -
288B LEU 4.0 4.4 + - - -
290B ILE* 3.6 15.7 - - + +
291B ASP 3.0 17.4 + - - +
292B ASP* 3.9 7.2 - - - +
294B LEU* 1.3 76.5 - - - +
296B ILE* 1.3 51.1 + - - +
298B LEU* 3.3 8.4 + - + +
299B LEU* 2.8 33.2 + - + +
346B MET* 3.4 15.0 - - - +
358B GLU* 2.9 38.8 + - - -
419B ARG* 3.8 19.2 - - - +
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Residues in contact with ILE 296 (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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90B ILE* 3.6 15.7 - - + -
124B ALA* 3.9 19.3 - - + +
125B TYR 3.5 31.4 - - - +
126B SER* 4.0 11.7 - - - +
134B GLN* 5.3 6.1 - - - +
135B PHE* 4.9 8.6 - - + +
292B ASP 2.9 24.8 + - - +
293B VAL* 3.8 7.6 - - - +
294B LEU 3.3 0.2 - - - -
295B ARG* 1.3 74.2 - - - +
297B GLN* 1.3 64.7 + - - +
299B LEU* 3.1 8.9 + - - +
300B LYS* 2.9 50.9 + - + +
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Residues in contact with GLN 297 (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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908A ASN* 5.9 2.8 - - - +
947A ARG* 6.2 0.6 - - - +
293B VAL* 3.2 26.3 + - + +
294B LEU* 3.2 11.8 + - + +
296B ILE* 1.3 79.5 - - - +
298B LEU* 1.3 61.8 - - - +
300B LYS* 3.2 53.9 + - - +
301B ILE* 3.5 14.2 + - - +
434B SER* 4.5 17.0 - - - +
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Residues in contact with LEU 298 (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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92B ILE* 6.0 1.3 - - + -
282B TYR* 6.0 0.3 - - - -
285B ALA* 3.9 35.7 - - + +
288B LEU* 4.9 3.4 - - + -
290B ILE* 3.9 21.8 - - + -
294B LEU 2.9 12.6 + - - +
295B ARG* 3.4 12.8 - - + +
297B GLN* 1.3 75.9 - - - +
299B LEU* 1.3 59.2 + - - +
301B ILE* 3.2 33.1 + - + +
307B ARG* 4.0 26.0 + - + +
310B CYS* 3.5 29.2 - - - -
311B GLU* 4.3 10.8 - - + +
314B ILE* 4.8 4.7 - - + -
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Residues in contact with LEU 299 (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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90B ILE* 4.2 11.2 - - + -
91B LEU 3.9 9.0 - - - +
92B ILE* 4.7 9.6 - - + -
93B PRO* 4.2 9.9 - - + -
124B ALA* 4.0 27.1 - - + -
135B PHE* 4.4 8.3 - - + -
136B GLY 4.0 16.6 - - - +
137B THR* 3.4 26.2 - - - +
164B ARG* 3.1 53.0 + - + +
185B LEU* 5.3 0.5 - - - +
282B TYR* 5.6 2.2 - - + -
295B ARG* 2.8 20.2 + - + +
296B ILE* 3.1 7.1 + - - +
298B LEU* 1.3 72.4 - - - +
300B LYS* 1.3 57.0 + - + +
301B ILE 3.3 0.9 + - - -
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Residues in contact with LYS 300 (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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134B GLN* 5.7 3.2 + - - -
135B PHE* 3.6 50.7 - - + -
164B ARG* 3.9 8.0 + - - +
185B LEU* 5.5 1.2 - - - +
296B ILE* 2.9 26.7 + - - +
297B GLN* 3.2 49.5 + - - +
299B LEU* 1.3 73.5 - - - +
301B ILE* 1.4 59.4 + - + +
302B GLY 3.5 2.4 + - - -
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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
------------------------------------------------------------
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