Contacts of the helix formed by residues 458 - 466 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147C SER* 4.9 0.8 + - - -
320C LYS* 5.0 2.2 - - - +
453C VAL* 4.0 21.6 + - + +
456C THR* 2.8 39.0 - - - +
457C PRO 3.7 9.4 + - - -
458C HIS* 3.4 28.5 + - + +
320I LYS* 5.6 0.2 - - - -
456I THR 3.3 1.4 + - - +
457I PRO* 1.3 72.5 - - - +
459I PRO* 1.3 72.8 - - + +
460I VAL* 2.9 51.7 - - + +
461I GLU* 2.7 53.1 + - + +
462I PHE* 3.5 6.1 - - - -
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Residues in contact with PRO 459 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C PHE* 4.4 5.7 - - - +
141C GLY 4.2 4.9 - - - +
147C SER* 3.7 12.6 - - - -
148C HIS* 3.6 41.1 - - - +
149C VAL* 4.2 10.7 - - + +
459C PRO* 3.7 30.5 - - + -
147I SER* 4.2 3.8 - - - +
457I PRO 4.0 5.6 - - - +
458I HIS* 1.3 91.6 - - + +
460I VAL* 1.3 56.7 + - + +
462I PHE* 3.0 33.9 + - + +
463I GLU* 3.5 4.5 + - - +
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Residues in contact with VAL 460 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142C ALA* 4.0 20.6 - - + -
452C ARG* 3.9 36.3 - - + +
453C VAL* 4.1 7.6 - - + -
456C THR* 3.7 22.0 - - + +
458I HIS* 2.9 27.8 - - + +
459I PRO* 1.3 74.0 - - + +
461I GLU* 1.3 59.0 + - - +
462I PHE 3.1 0.2 - - - -
463I GLU* 3.2 9.1 + - - +
464I LEU* 3.0 46.1 + - + +
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Residues in contact with GLU 461 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256C MET* 3.9 6.2 - - + +
316C THR* 2.7 29.0 + - - +
317C ASN* 2.9 36.7 + - - +
320C LYS* 2.7 32.8 + - - +
453C VAL* 4.1 9.5 - - + +
458I HIS* 2.7 43.9 + - + +
460I VAL* 1.3 72.5 - - - +
462I PHE* 1.3 52.9 + - + +
464I LEU* 4.8 0.2 - - - -
465I TYR* 2.7 51.4 + - + +
466I TYR 3.9 0.3 + - - -
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Residues in contact with PHE 462 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C ILE* 4.0 18.4 - - + -
140C PHE* 3.6 25.7 - - + -
149C VAL* 3.7 40.4 - - + -
151C ILE* 4.3 3.6 - - + -
256C MET* 3.4 34.3 - - + -
259C PRO* 3.3 32.8 - - + -
457I PRO* 4.0 15.5 - - + -
458I HIS 3.5 18.6 - - - -
459I PRO 3.0 10.2 + - - +
461I GLU* 1.3 78.1 - - + +
463I GLU* 1.3 65.5 + - - +
466I TYR* 3.0 33.7 + + - +
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Residues in contact with GLU 463 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160B SER* 4.7 3.8 + - - -
140C PHE* 3.5 24.2 - - + -
141C GLY* 4.2 7.9 - - - -
142C ALA* 4.0 27.1 + - - +
452C ARG* 2.7 44.7 + - - +
459I PRO 3.5 2.2 + - - +
460I VAL* 3.2 15.6 + - - +
462I PHE* 1.3 80.4 - - - +
464I LEU* 1.3 61.5 + - + +
466I TYR 5.0 0.2 + - - -
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Residues in contact with LEU 464 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449C GLU* 3.6 46.2 - - + +
452C ARG* 4.1 32.3 - - + +
453C VAL* 3.7 18.4 - - + -
460I VAL* 3.0 23.2 + - + +
463I GLU* 1.3 81.2 - - + +
465I TYR* 1.3 87.4 + - + +
466I TYR 4.0 0.2 - - - -
467I SER 5.6 0.2 - - - -
468I VAL* 5.2 1.9 - - - +
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Residues in contact with TYR 465 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256C MET* 3.5 19.8 - - + +
257C PRO* 5.4 0.9 - - + -
314C PRO 4.7 0.4 - - - -
315C THR* 3.4 44.1 - - + -
316C THR* 3.4 39.6 + - - +
317C ASN* 4.0 6.7 - - + -
414C LEU* 4.5 2.4 - - - +
446C ARG* 4.8 2.9 - - - -
449C GLU* 3.7 38.6 + - - +
461I GLU* 2.7 39.8 + - + +
464I LEU* 1.3 100.6 - - + +
466I TYR* 1.3 65.3 + - - +
467I SER 3.2 3.6 - - - -
468I VAL* 3.0 30.0 + - + +
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Residues in contact with TYR 466 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169B LYS 3.9 2.7 - - - -
170B GLY 4.0 11.7 - - - +
171B HIS* 3.4 30.4 - + - -
135C PHE* 3.8 10.7 - + - -
138C ILE* 3.6 42.5 - - + +
140C PHE* 4.4 6.5 - + + -
243C HIS* 4.9 0.2 + - - -
252C THR* 2.8 42.9 + - - +
253C ALA 4.2 0.6 + - - -
254C THR* 2.8 52.1 + - + -
255C PHE 4.3 1.4 + - - -
256C MET* 3.6 18.6 - - - +
461I GLU 3.9 0.8 + - - -
462I PHE* 3.0 27.0 + + - +
463I GLU 5.0 0.2 - - - -
464I LEU 4.0 0.2 - - - -
465I TYR* 1.3 77.8 - - - +
467I SER* 1.3 57.3 + - - +
468I VAL 3.3 2.8 + - - -
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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