Contacts of the helix formed by residues 458 - 466 (chain G) in PDB entry 1F1H
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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A SER* 5.0 0.4 + - - -
320A LYS* 4.9 2.5 - - - +
453A VAL* 4.0 23.4 + - + +
456A THR* 2.9 35.7 + - - +
457A PRO 3.7 10.0 + - - -
458A HIS* 3.3 30.5 + - + +
320G LYS* 5.2 0.6 - - - -
456G THR 3.3 1.0 + - - +
457G PRO* 1.3 72.9 - - - +
459G PRO* 1.3 72.4 - - + +
460G VAL* 2.9 51.0 - - + +
461G GLU* 2.7 52.5 + - + +
462G PHE* 3.5 6.1 - - - -
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Residues in contact with PRO 459 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A PHE* 4.4 6.1 - - - +
141A GLY 4.3 4.7 - - - +
147A SER* 3.7 11.7 - - - -
148A HIS* 3.6 37.9 - - - +
149A VAL* 4.2 11.4 - - + -
458A HIS* 4.9 0.2 - - + -
459A PRO* 3.7 34.8 - - + -
147G SER* 4.2 4.3 - - - +
457G PRO 4.0 5.4 - - - +
458G HIS* 1.3 92.2 - - + +
460G VAL* 1.3 56.6 - - + +
462G PHE* 3.0 33.7 + - + +
463G GLU* 3.5 4.2 + - - +
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Residues in contact with VAL 460 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ALA* 4.0 20.6 - - + -
147A SER* 5.4 0.2 - - - -
452A ARG* 4.0 35.0 - - + +
453A VAL* 4.0 7.9 - - + -
456A THR* 3.7 22.0 - - + +
458G HIS* 2.9 28.6 - - + +
459G PRO* 1.3 73.4 - - + +
461G GLU* 1.3 59.4 + - - +
462G PHE 3.1 0.2 - - - -
463G GLU* 3.2 9.9 + - - +
464G LEU* 3.0 46.1 + - + +
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Residues in contact with GLU 461 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A MET* 3.8 4.6 - - + +
316A THR* 2.7 28.3 + - - +
317A ASN* 2.8 40.8 + - + +
320A LYS* 2.7 35.4 + - - +
453A VAL* 4.2 7.5 - - + +
458G HIS* 2.7 42.1 + - + +
460G VAL* 1.3 72.7 - - - +
462G PHE* 1.3 55.1 + - + +
464G LEU* 4.3 0.9 - - - -
465G TYR* 2.7 50.9 + - + +
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Residues in contact with PHE 462 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 5.8 0.2 - + - -
138A ILE* 4.0 15.0 - - + -
140A PHE* 3.6 25.8 - - + -
149A VAL* 3.6 39.9 - - + -
151A ILE* 4.2 7.2 - - + -
256A MET* 3.4 35.4 - - + -
259A PRO* 3.2 33.4 - - + -
457G PRO* 4.0 15.5 - - + -
458G HIS 3.5 17.5 - - - -
459G PRO 3.0 10.0 + - - +
461G GLU* 1.3 79.3 - - + +
463G GLU* 1.3 63.9 + - - +
466G TYR* 3.0 35.0 + + + +
467G SER 4.9 0.2 + - - -
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Residues in contact with GLU 463 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A PHE* 3.4 24.4 - - + -
141A GLY* 4.1 8.2 - - - -
142A ALA* 3.9 27.0 + - - +
452A ARG* 2.8 44.6 + - - +
160F SER* 4.6 4.2 + - - -
459G PRO 3.5 2.6 + - - +
460G VAL* 3.2 16.3 + - - +
462G PHE* 1.3 79.8 - - - +
464G LEU* 1.3 61.1 + - + +
466G TYR 5.0 0.3 + - - -
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Residues in contact with LEU 464 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A GLU* 3.6 46.5 - - + +
452A ARG* 4.1 32.1 - - + +
453A VAL* 3.7 18.8 - - + -
460G VAL* 3.0 23.4 + - + +
463G GLU* 1.3 81.9 - - + +
465G TYR* 1.3 88.9 + - + +
467G SER 5.5 0.4 + - - -
468G VAL* 5.2 1.9 - - - +
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Residues in contact with TYR 465 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A MET* 3.4 18.1 - - + +
257A PRO* 5.4 0.9 - - + -
315A THR* 3.4 44.2 - - + -
316A THR* 3.3 38.8 + - - +
317A ASN* 4.0 7.2 - - + -
414A LEU* 4.5 2.3 - - - +
446A ARG* 4.8 3.4 - - - -
449A GLU* 3.8 37.3 + - - +
461G GLU* 2.7 38.9 + - + +
464G LEU* 1.3 100.3 - - + +
466G TYR* 1.3 67.4 + - - +
467G SER 3.2 2.9 - - - -
468G VAL* 3.0 31.9 + - + +
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Residues in contact with TYR 466 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A PHE* 3.7 12.2 - + - -
138A ILE* 3.5 43.0 - - + +
140A PHE* 4.3 7.2 - + + -
243A HIS* 4.9 0.2 + - - -
252A THR* 2.8 49.7 + - - +
253A ALA 4.3 1.0 - - - -
254A THR* 2.8 52.2 + - + -
255A PHE 4.3 0.7 + - - -
256A MET* 3.6 17.7 - - - +
169F LYS 3.9 3.4 - - - -
170F GLY 4.0 13.0 - - - +
171F HIS* 3.6 22.0 - + - -
461G GLU 3.9 0.8 + - - -
462G PHE* 3.0 28.7 + + - +
464G LEU 4.0 0.2 - - - -
465G TYR* 1.3 77.3 - - - +
467G SER* 1.3 57.6 + - - +
468G VAL 3.2 3.5 + - - +
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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