Contacts of the strand formed by residues 295 - 302 (chain A) in PDB entry 2FPM
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 LYS 295 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A GLY* 2.7 29.8 + - - -
292A LYS* 2.9 30.6 + - + +
294A ASP* 1.3 83.8 + - - +
296A ARG* 1.3 66.3 + - - +
297A VAL* 6.2 0.7 - - + -
312A ILE* 4.2 22.5 - - + +
313A PHE 3.5 5.6 - - - +
314A ARG* 3.7 20.9 - - + +
322A ASP* 3.6 22.2 + - - -
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Residues in contact with ARG 296 (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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108A GLY 3.3 20.9 + - - -
109A SER 3.2 26.5 + - - +
288A VAL* 6.1 0.4 - - + -
289A ARG 3.3 14.1 - - - +
290A LYS* 3.7 19.5 - - - +
291A GLY 4.2 0.7 - - - +
293A GLY 3.0 23.2 + - - -
294A ASP* 3.3 15.0 - - - +
295A LYS* 1.3 90.4 + - - +
297A VAL* 1.3 66.6 + - - +
312A ILE* 3.4 6.1 - - - +
313A PHE* 2.7 57.7 + - + +
315A ILE* 3.7 27.2 - - + +
401A ANP 4.0 23.8 + - - -
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Residues in contact with VAL 297 (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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287A PHE 3.5 2.6 - - - +
288A VAL* 3.3 2.5 - - - -
289A ARG* 2.7 86.4 + - + +
291A GLY* 5.3 10.3 - - - +
295A LYS* 6.2 0.4 - - + -
296A ARG* 1.3 81.0 - - - +
298A ALA* 1.3 60.7 + - - +
299A LYS 3.8 0.2 + - - -
310A GLU* 3.7 23.8 - - + +
311A ALA 3.3 9.4 - - - +
312A ILE* 4.3 16.6 - - + -
313A PHE* 4.3 1.8 - - - -
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Residues in contact with ALA 298 (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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87A LEU* 4.0 18.8 - - + -
90A VAL* 5.2 0.2 - - - +
103A PHE* 4.9 1.6 - - + -
286A PHE* 3.9 19.2 - - + -
287A PHE 3.6 4.3 - - - -
288A VAL* 4.3 12.1 - - + +
297A VAL* 1.3 71.4 - - - +
299A LYS* 1.3 60.7 + - - +
300A LEU 3.9 0.7 + - - -
309A ALA 3.8 1.2 - - - +
310A GLU* 3.3 2.8 - - - -
311A ALA* 2.8 39.9 + - + +
313A PHE* 3.9 18.9 - - + -
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Residues in contact with LYS 299 (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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286A PHE* 3.3 5.5 - - - -
287A PHE* 2.8 49.8 + - + +
289A ARG* 4.2 12.3 - - - +
297A VAL 3.8 0.2 + - - -
298A ALA* 1.3 71.4 - - - +
300A LEU* 1.3 77.9 + - - +
301A TYR* 3.4 17.1 + - + +
308A ASP* 3.4 26.5 + - - +
309A ALA* 3.5 9.9 - - - +
310A GLU* 3.4 33.4 - - + +
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Residues in contact with LEU 300 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A VAL* 3.6 31.0 - - + +
284A PHE* 4.3 9.4 - - + -
285A ARG 3.5 13.7 - - - +
286A PHE* 3.6 37.9 - - + -
298A ALA 3.9 0.2 + - - -
299A LYS* 1.3 84.4 + - - +
301A TYR* 1.3 58.5 + - - +
302A ASP 3.4 26.0 - - - +
303A SER* 4.1 7.2 - - - +
306A LEU* 4.1 17.5 - - + -
307A PRO 3.7 21.1 - - - +
308A ASP* 3.3 16.5 - - - +
309A ALA 2.9 10.0 + - - +
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Residues in contact with TYR 301 (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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102A GLU* 4.6 1.0 + - - -
272A ALA* 4.0 5.9 + - - +
285A ARG* 3.0 78.8 + - + +
286A PHE 3.6 15.1 + - - -
287A PHE* 3.3 48.7 - + + -
299A LYS* 3.6 25.1 - - + +
300A LEU* 1.3 72.6 - - - +
302A ASP* 1.3 63.8 + - + +
308A ASP* 3.5 21.1 - - - +
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Residues in contact with ASP 302 (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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279A GLY 4.1 9.0 - - - +
282A ALA 4.2 6.6 - - - +
283A THR 4.2 2.0 - - - +
284A PHE* 3.4 2.9 - - - -
285A ARG* 3.0 59.8 + - + +
300A LEU* 3.4 6.5 - - - +
301A TYR* 1.3 85.6 - - + +
303A SER* 1.3 73.9 + - - +
308A ASP* 4.1 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
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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