Contacts of the helix formed by residues 316 - 321 (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 THR 316 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461D GLU* 2.6 35.1 + - - +
465D TYR* 3.4 16.0 + - - +
315J THR* 1.3 71.9 - - - +
317J ASN* 1.3 61.8 + - - +
319J TYR* 3.3 24.6 + - - +
320J LYS* 3.7 10.8 + - - -
414J LEU* 4.0 11.4 - - + +
450J ASP* 3.2 35.9 - - - +
453J VAL* 3.5 21.9 - - + +
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Residues in contact with ASN 317 (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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457D PRO* 4.2 4.6 - - - +
461D GLU* 3.0 32.3 + - + -
465D TYR* 4.1 13.7 - - + -
256J MET* 3.5 18.7 - - + +
257J PRO* 3.2 13.2 - - + +
258J LYS* 2.7 52.7 + - - +
315J THR* 3.6 7.6 - - - +
316J THR* 1.3 79.7 + - - +
318J SER* 1.3 65.8 + - - +
320J LYS* 2.9 21.9 + - - +
321J ARG 3.8 2.3 + - - -
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Residues in contact with SER 318 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257J PRO* 3.6 8.4 - - - +
313J ASN* 3.6 21.3 - - - -
315J THR* 2.6 41.3 + - - +
317J ASN* 1.3 76.7 - - - +
319J TYR* 1.3 58.7 + - - +
320J LYS 3.2 0.2 - - - -
321J ARG* 3.2 19.6 + - - +
322J LEU* 3.3 16.2 + - - +
362J ASP* 2.7 33.7 + - - +
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Residues in contact with TYR 319 (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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454D ARG* 4.7 8.9 + - - +
309J ASN* 3.5 8.8 + - + +
313J ASN* 2.8 27.4 + - + +
315J THR 3.2 21.5 - - - -
316J THR* 3.6 10.5 - - - +
317J ASN 3.1 1.0 - - - -
318J SER* 1.3 73.8 - - - +
320J LYS* 1.3 62.2 + - - +
321J ARG 3.3 1.3 - - - -
322J LEU* 3.4 39.7 - - + +
323J VAL* 4.2 8.1 - - - +
411J ALA* 3.5 30.7 - - + -
412J GLY* 4.0 13.5 - - - +
413J SER* 3.7 19.7 - - - -
414J LEU* 3.3 28.4 - - + -
417J ALA* 3.3 21.3 - - - +
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Residues in contact with LYS 320 (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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453D VAL 4.2 4.4 + - - -
454D ARG* 3.1 30.4 + - - +
455D MET* 3.9 13.7 - - - +
456D THR 3.3 23.3 - - - +
457D PRO* 3.7 14.6 - - + -
458D HIS* 4.4 4.0 - - - +
461D GLU* 2.7 41.3 + - - +
258J LYS* 3.4 29.2 - - + -
316J THR* 3.7 10.8 + - - +
317J ASN* 2.9 13.6 + - - +
319J TYR* 1.3 79.4 - - + +
321J ARG* 1.3 60.0 + - - +
323J VAL* 4.0 15.8 - - - +
453J VAL* 5.0 5.7 - - - +
458J HIS* 5.6 0.2 - - - -
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Residues in contact with ARG 321 (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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257J PRO* 4.1 20.4 - - + +
258J LYS* 4.1 12.6 + - + +
265J GLY* 4.5 9.2 - - - +
266J SER 3.4 26.9 + - - +
267J GLY* 3.4 23.3 - - - +
268J MET 4.4 0.2 - - - +
269J HIS* 4.5 7.3 + - - -
313J ASN* 4.1 1.4 + - - -
317J ASN 3.8 1.0 + - - -
318J SER 3.2 11.4 + - - +
320J LYS* 1.3 78.9 - - - +
322J LEU* 1.3 71.0 + - + +
323J VAL* 2.9 15.7 + - - +
328J ALA* 4.0 12.5 - - - +
329J PRO* 4.2 13.8 - - + +
359J ARG 3.3 21.8 + - - -
360J PHE 2.9 25.3 + - - -
361J PRO 3.5 5.7 + - - -
362J ASP* 3.9 7.5 + - - +
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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