Contacts of the helix formed by residues 458 - 466 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D SER* 4.9 1.0 + - - -
320D LYS* 5.0 2.0 - - - -
453D VAL* 4.0 22.3 + - + +
456D THR* 2.8 39.5 - - - +
457D PRO 3.7 8.7 + - - -
458D HIS* 3.4 30.5 + - + +
320J LYS* 5.2 0.4 - - - -
456J THR 3.3 1.2 + - - +
457J PRO* 1.3 72.1 - - - +
459J PRO* 1.3 73.1 - - + +
460J VAL* 2.9 51.1 - - + +
461J GLU* 2.7 54.5 + - + +
462J PHE* 3.5 6.3 - - - -
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Residues in contact with PRO 459 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D PHE* 4.4 5.7 - - - +
141D GLY 4.2 5.3 + - - +
142D ALA* 5.8 0.2 - - - -
147D SER* 3.6 12.8 - - - -
148D HIS* 3.6 43.7 - - - +
149D VAL* 4.3 7.6 - - + +
459D PRO* 3.7 30.7 - - + -
147J SER* 4.2 3.4 - - - +
457J PRO 4.0 5.2 - - - +
458J HIS* 1.3 90.7 - - + +
460J VAL* 1.3 56.3 + - + +
462J PHE* 3.0 34.1 + - + +
463J GLU* 3.5 4.2 + - - +
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Residues in contact with VAL 460 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142D ALA* 3.9 19.7 - - + -
452D ARG* 3.9 36.3 - - + +
453D VAL* 4.1 7.6 - - + -
456D THR* 3.7 22.7 - - + +
458J HIS* 2.9 29.8 - - + +
459J PRO* 1.3 73.8 - - + +
461J GLU* 1.3 57.0 + - - +
462J PHE 3.1 0.2 - - - -
463J GLU* 3.2 8.6 + - - +
464J LEU* 3.0 45.5 + - + +
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Residues in contact with GLU 461 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D MET* 4.0 2.9 - - + +
316D THR* 2.6 29.1 + - - +
317D ASN* 3.0 37.1 + - + +
320D LYS* 2.7 31.5 + - - +
453D VAL* 4.0 8.6 - - + +
457J PRO* 3.5 0.2 - - - +
458J HIS* 2.7 43.8 + - + +
460J VAL* 1.3 72.7 - - - +
462J PHE* 1.3 56.3 + - + +
464J LEU* 4.3 0.9 - - - -
465J TYR* 2.7 50.9 + - + +
466J TYR 3.9 0.2 + - - -
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Residues in contact with PHE 462 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D PHE* 6.0 0.2 - + - -
138D ILE* 4.1 18.8 - - + -
140D PHE* 3.6 25.7 - - + -
149D VAL* 3.7 40.2 - - + -
151D ILE* 4.4 2.9 - - + -
256D MET* 3.4 34.5 - - + -
259D PRO* 3.4 32.1 - - + -
457J PRO* 4.0 16.6 - - + -
458J HIS 3.5 16.8 - - - -
459J PRO 3.0 10.7 + - - +
461J GLU* 1.3 79.3 - - + +
463J GLU* 1.3 65.3 + - - +
464J LEU 3.2 0.2 - - - -
466J TYR* 3.0 34.3 + + + +
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Residues in contact with GLU 463 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160C SER* 4.8 3.8 + - - -
140D PHE* 3.5 23.1 - - + -
141D GLY* 4.2 7.7 - - - -
142D ALA* 4.0 28.5 + - - +
452D ARG* 2.7 45.2 + - - +
459J PRO 3.5 2.2 + - - +
460J VAL* 3.2 15.5 + - - +
462J PHE* 1.3 79.1 - - - +
464J LEU* 1.3 60.8 + - + +
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Residues in contact with LEU 464 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449D GLU* 3.5 47.1 - - + +
452D ARG* 4.0 32.1 - - + +
453D VAL* 3.7 17.9 - - + -
460J VAL* 3.0 24.5 + - + +
463J GLU* 1.3 80.7 - - + +
465J TYR* 1.3 89.8 + - + +
466J TYR 4.0 0.2 - - - -
468J VAL* 5.2 1.7 - - - +
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Residues in contact with TYR 465 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256D MET* 3.6 17.9 - - + +
257D PRO* 5.5 1.6 - - + -
314D PRO 4.7 0.2 - - - -
315D THR* 3.5 45.6 - - + -
316D THR* 3.4 38.8 + - - +
317D ASN* 4.1 7.0 - - + -
414D LEU* 4.5 2.8 - - - +
446D ARG* 4.8 3.1 - - - -
449D GLU* 3.6 40.3 + - - +
461J GLU* 2.7 39.1 + - + +
464J LEU* 1.3 100.4 - - + +
466J TYR* 1.3 66.2 + - - +
467J SER 3.2 3.4 - - - -
468J VAL* 3.0 31.4 + - + +
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Residues in contact with TYR 466 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C LYS 4.0 2.7 - - - -
170C GLY 3.9 13.2 - - - -
171C HIS* 3.4 28.0 - + - -
135D PHE* 3.9 9.6 - + - -
138D ILE* 3.5 39.9 - - + +
140D PHE* 4.3 9.9 - + + -
243D HIS* 5.0 0.2 + - - -
252D THR* 2.7 42.4 + - - +
253D ALA 4.2 0.6 + - - -
254D THR* 2.9 51.9 + - + -
255D PHE 4.4 1.2 + - - -
256D MET* 3.7 18.8 - - - +
461J GLU 3.9 0.8 + - - -
462J PHE* 3.0 29.1 + + - +
463J GLU 5.0 0.2 + - - -
464J LEU 4.0 0.2 - - - -
465J TYR* 1.3 77.7 - - - +
467J SER* 1.3 58.4 + - - +
468J 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