Contacts of the helix formed by residues 458 - 466 (chain E) in PDB entry 1FPY
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 HIS 458 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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320E LYS* 5.2 1.4 + - - -
456E THR 3.4 1.0 + - - -
457E PRO* 1.3 73.4 - - - +
459E PRO* 1.3 80.4 - - + +
460E VAL* 2.9 40.9 - - + +
461E GLU* 2.8 40.1 + - + +
462E PHE* 3.4 7.7 - - - -
147K SER* 4.7 0.6 + - - -
320K LYS* 4.5 3.1 - - - +
453K VAL* 4.2 19.5 + - + +
456K THR* 2.8 51.1 - - - +
457K PRO 3.1 14.5 + - - -
458K HIS* 3.1 30.6 + - + +
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Residues in contact with PRO 459 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147E SER* 4.1 6.5 - - - +
457E PRO 4.1 3.8 - - - +
458E HIS* 1.3 92.1 - - + +
460E VAL* 1.3 52.7 + - - +
462E PHE* 2.7 42.6 + - + +
463E GLU* 3.5 3.0 + - - +
140K PHE* 4.5 4.5 - - - +
141K GLY 4.3 4.0 - - - +
147K SER* 3.8 14.8 - - - +
148K HIS* 3.5 39.3 - - - +
149K VAL* 4.2 3.3 - - + +
459K PRO* 3.5 36.8 - - + -
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Residues in contact with VAL 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458E HIS* 2.9 29.5 - - + +
459E PRO* 1.3 76.4 - - + +
461E GLU* 1.3 56.2 + - - +
463E GLU* 3.1 10.5 + - + +
464E LEU* 2.8 49.2 + - + +
142K ALA* 4.1 14.1 - - + -
452K ARG* 4.1 33.7 - - + +
453K VAL* 4.1 11.0 - - + +
456K THR* 3.7 22.4 - - + +
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Residues in contact with GLU 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457E PRO* 3.6 0.3 - - - +
458E HIS* 2.8 37.0 + - + +
460E VAL* 1.3 77.1 - - - +
462E PHE* 1.3 53.7 + - + +
465E TYR* 2.5 52.6 + - + +
256K MET* 3.9 4.5 - - + +
316K THR* 2.7 27.2 + - - +
317K ASN* 2.8 43.9 + - - +
320K LYS* 3.0 34.5 + - - +
453K VAL* 4.1 6.8 - - + +
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Residues in contact with PHE 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457E PRO* 4.0 15.5 - - + -
458E HIS 3.4 13.0 - - - -
459E PRO 2.7 16.1 + - - +
461E GLU* 1.3 75.3 - - + +
463E GLU* 1.3 69.1 + - - +
466E TYR* 2.9 41.7 + + + +
467E SER 4.7 0.2 + - - -
138K ILE* 4.4 5.6 - - + -
140K PHE* 3.6 27.6 - - + -
149K VAL* 3.5 38.4 - - + -
151K ILE* 4.4 7.9 - - + -
256K MET* 3.4 30.5 - - + -
259K PRO* 3.2 36.6 - - + -
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Residues in contact with GLU 463 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459E PRO 3.5 1.8 + - - +
460E VAL* 3.3 15.1 - - - +
462E PHE* 1.3 82.2 - - - +
464E LEU* 1.3 62.2 + - + +
467E SER 5.9 0.3 + - - -
140K PHE* 3.3 25.9 - - + -
141K GLY* 4.6 3.5 - - - -
142K ALA* 3.9 25.1 + - - +
452K ARG* 2.6 41.5 + - - +
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Residues in contact with LEU 464 (chain E).
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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460E VAL* 2.8 31.5 + - + +
463E GLU* 1.3 81.9 - - + +
465E TYR* 1.3 86.1 + - + +
466E TYR 3.9 0.2 - - - -
468E VAL* 5.2 2.1 + - - +
449K GLU* 3.6 44.3 - - + +
452K ARG* 3.6 33.7 - - + +
453K VAL* 3.8 11.2 - - + -
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Residues in contact with TYR 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461E GLU* 2.5 41.8 + - + +
464E LEU* 1.3 99.1 - - + +
466E TYR* 1.3 65.7 + - - +
467E SER 3.2 3.1 - - - -
468E VAL* 2.9 35.1 + - + +
256K MET* 3.8 17.4 - - + +
257K PRO* 5.6 0.7 - - + -
314K PRO 4.2 1.4 + - - -
315K THR* 3.4 43.3 - - + -
316K THR* 3.3 39.8 + - - +
317K ASN* 4.2 4.9 - - + -
414K LEU* 4.5 1.6 - - - +
446K ARG* 4.6 2.9 - - - -
449K GLU* 3.4 41.4 + - - +
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Residues in contact with TYR 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461E GLU 3.8 1.8 + - - -
462E PHE* 2.9 30.1 + + - +
463E GLU 5.0 0.2 + - - -
465E TYR* 1.3 76.8 - - - +
467E SER* 1.3 63.2 + - - +
468E VAL 3.1 4.5 + - - +
135K PHE* 3.8 12.2 - + - -
138K ILE* 3.5 42.8 - - + +
140K PHE* 4.4 7.4 - + + -
243K HIS* 4.9 0.3 + - - -
252K THR* 2.6 38.8 + - - +
253K ALA 4.0 1.2 + - - -
254K THR* 2.8 55.2 + - + -
255K PHE 4.2 1.7 + - - -
256K MET* 3.8 14.8 - - - -
169L LYS 4.4 2.5 - - - -
170L GLY 4.4 7.9 - - - -
171L HIS* 3.3 30.7 - + - -
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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