Contacts of the helix formed by residues 366 - 384 (chain H) 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 ASN 366 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H THR* 4.1 1.0 - - - +
23H ASP 3.3 16.0 + - - -
24H THR 2.8 25.9 + - - +
25H LYS 4.0 5.7 + - - +
26H GLY* 3.4 18.0 - - - -
104H PRO* 3.8 7.7 - - - +
311H LEU 4.0 4.9 + - - +
314H PRO* 4.8 1.6 - - - +
364H ALA 3.6 2.4 + - - -
365H ALA* 1.3 70.2 - - - +
367H PRO* 1.3 69.2 - - - +
368H TYR* 3.0 27.9 + - - +
369H LEU* 3.6 25.5 - - + +
370H CYS* 2.8 24.7 + - - +
442H TYR* 5.6 2.7 + - + +
446H ARG* 5.2 2.2 - - - +
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Residues in contact with PRO 367 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26H GLY 4.7 2.0 - - - +
232H ALA* 3.7 34.1 - - + +
235H ILE* 3.8 22.9 - - + -
236H GLN* 3.7 26.5 - - - +
239H LYS* 4.5 3.4 - - - +
268H MET* 5.2 3.1 - - + -
365H ALA 3.0 10.9 - - - +
366H ASN* 1.3 86.0 - - - +
368H TYR* 1.3 60.3 + - + +
370H CYS* 4.5 2.0 - - + -
371H PHE* 2.9 49.9 + - + -
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Residues in contact with TYR 368 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H THR* 3.4 27.8 + - + -
88H ARG* 3.8 13.9 + - - -
104H PRO* 3.3 33.2 - - + +
105H ARG* 3.9 23.3 + - + -
108H ALA* 4.0 22.1 - - + +
229H THR* 4.0 6.3 - - + -
232H ALA* 3.3 26.5 + - + -
233H ASP* 2.6 36.8 + - - -
236H GLN* 4.1 11.1 - - + +
366H ASN* 3.0 14.0 + - - +
367H PRO* 1.3 80.3 - - + +
369H LEU* 1.3 60.4 + - - +
371H PHE* 3.9 1.5 - - - +
372H ALA* 2.9 33.0 + - - +
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Residues in contact with LEU 369 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H THR* 3.8 25.6 - - + +
104H PRO* 3.8 27.4 - - + -
107H ILE* 3.8 24.9 - - + -
311H LEU* 3.5 20.1 - - + +
366H ASN* 3.3 19.5 + - + +
368H TYR* 1.3 79.7 - - - +
370H CYS* 1.3 57.9 + - - +
372H ALA* 3.9 4.5 - - - +
373H ALA* 3.0 31.2 + - - +
434H PHE* 4.2 13.4 - - + -
442H TYR* 3.8 27.8 - - + -
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Residues in contact with CYS 370 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268H MET* 4.9 2.0 - - - -
270H CYS* 5.0 0.2 - - - -
308H ILE* 4.9 1.1 - - - +
311H LEU* 3.7 23.5 - - - +
312H ALA* 3.5 31.2 - - - -
361H PRO* 4.3 8.5 - - - -
365H ALA* 3.9 10.1 - - + -
366H ASN 2.8 22.4 + - - +
367H PRO* 4.0 2.2 - - + +
369H LEU* 1.3 73.0 - - - +
371H PHE* 1.3 74.0 + - + +
373H ALA* 3.3 2.9 + - - +
374H LEU* 3.0 35.9 + - - +
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Residues in contact with PHE 371 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H PHE* 3.3 36.2 - + + -
128H PRO* 3.4 31.0 - - + -
228H MET* 3.6 36.2 - - + +
231H LYS* 4.1 7.0 - - + -
232H ALA* 3.8 28.7 - - + -
235H ILE* 4.2 3.1 - - + -
268H MET* 4.3 13.2 - - + -
270H CYS* 4.0 21.3 - - - -
367H PRO* 2.9 33.1 + - + +
368H TYR* 3.9 2.2 - - - +
370H CYS* 1.3 82.6 - - - +
372H ALA* 1.3 62.6 + - - +
374H LEU* 3.2 2.4 + - - -
375H LEU 3.1 17.8 + - - -
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Residues in contact with ALA 372 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H ILE* 4.5 4.3 - - + -
108H ALA* 4.4 8.1 - - - -
111H ALA* 4.2 17.5 - - + -
228H MET* 3.7 15.2 - - + -
368H TYR 2.9 19.1 + - - +
369H LEU 3.9 3.1 - - - +
371H PHE* 1.3 75.8 - - - +
373H ALA* 1.3 58.9 + - - +
375H LEU* 3.1 4.3 + - - +
376H MET* 2.9 34.1 + - - +
434H PHE* 4.1 17.7 - - + -
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Residues in contact with ALA 373 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308H ILE* 4.1 14.6 - - + +
311H LEU* 3.7 27.6 - - + -
369H LEU 3.0 20.1 + - - +
370H CYS 3.6 4.0 - - - +
371H PHE 3.3 0.2 - - - -
372H ALA* 1.3 76.9 - - - +
374H LEU* 1.3 63.9 + - - +
377H ALA* 3.2 24.6 + - - +
427H PHE* 3.7 4.9 - - - -
428H LEU* 3.9 20.0 - - + -
434H PHE* 4.6 2.1 - - + -
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Residues in contact with LEU 374 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126H PHE* 4.1 12.1 - - + -
270H CYS* 4.5 10.3 - - + -
272H MET* 3.9 24.7 - - + -
297H TYR* 3.8 6.1 + - - -
301H VAL* 4.2 22.5 - - + +
308H ILE* 3.5 33.2 - - + -
358H VAL* 4.5 11.9 - - + -
360H PHE* 4.7 0.9 - - + -
361H PRO* 4.5 11.7 - - + -
370H CYS* 3.0 38.3 + - - +
371H PHE 3.2 8.5 + - - +
373H ALA* 1.3 77.7 - - - +
375H LEU* 1.3 61.6 + - - +
377H ALA* 3.3 3.5 + - - +
378H GLY* 3.0 17.7 + - - -
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Residues in contact with LEU 375 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H ALA* 3.7 32.3 - - + +
115H LEU* 4.4 5.2 - - + -
124H VAL* 3.7 40.6 - - + -
126H PHE* 4.6 1.1 - - + -
228H MET* 4.2 10.8 - - - -
274H LEU* 4.4 3.8 - - + -
297H TYR* 3.3 20.6 + - + +
371H PHE 3.1 8.7 + - - +
372H ALA 3.3 8.5 - - - +
374H LEU* 1.3 76.4 - - - +
376H MET* 1.3 56.3 + - - +
378H GLY* 2.8 4.0 + - - -
379H LEU* 2.8 59.9 + - + +
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Residues in contact with MET 376 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111H ALA* 4.1 16.4 - - + +
114H TYR* 4.1 21.5 - - + -
372H ALA 2.9 26.9 + - - +
373H ALA 4.1 0.2 - - - +
375H LEU* 1.3 74.0 - - - +
377H ALA* 1.3 56.0 + - - +
379H LEU* 3.9 7.9 - - - +
380H ASP* 3.1 26.9 + - - +
427H PHE* 3.5 30.0 - - - +
428H LEU* 3.7 24.9 - - + +
430H ALA* 3.2 34.1 - - + +
433H VAL* 3.5 25.4 - - + -
434H PHE* 4.8 0.7 - - + -
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Residues in contact with ALA 377 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300H GLY* 3.2 27.0 - - - +
301H VAL* 4.2 0.9 - - - -
304H HIS* 4.0 4.7 - - + -
308H ILE* 3.6 20.2 - - + -
373H ALA 3.2 19.3 + - - +
374H LEU 3.5 4.5 - - - +
375H LEU 3.1 0.6 - - - -
376H MET* 1.3 73.0 - - - +
378H GLY* 1.3 66.6 + - - +
380H ASP* 3.3 4.0 + - - +
381H GLY 3.1 16.3 + - - -
427H PHE* 3.5 21.3 - - + -
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Residues in contact with GLY 378 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297H TYR* 3.5 52.4 - - - -
301H VAL* 4.5 0.8 - - - +
374H LEU 3.0 7.8 + - - -
375H LEU 2.8 7.4 + - - -
377H ALA* 1.3 78.1 - - - +
379H LEU* 1.3 55.6 + - - +
381H GLY* 3.0 14.7 + - - -
382H ILE* 3.0 12.8 + - - +
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Residues in contact with LEU 379 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TYR* 3.7 38.4 - - + +
115H LEU* 3.4 38.1 - - + -
118H THR* 5.0 2.2 - - - +
120H ILE* 4.2 19.0 - - + +
274H LEU* 4.3 13.9 - - + -
375H LEU* 2.8 39.9 + - + +
376H MET* 3.9 8.7 - - - +
378H GLY* 1.3 72.9 - - - +
380H ASP* 1.3 60.2 + - - +
381H GLY 3.0 1.8 - - - -
382H ILE* 3.2 5.3 + - + +
383H LYS* 2.8 37.6 + - + +
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Residues in contact with ASP 380 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303H LYS* 4.4 5.0 + - - -
304H HIS* 2.9 29.4 + - - +
376H MET 3.1 18.6 + - - +
377H ALA 3.6 5.6 - - - +
378H GLY 3.3 0.2 - - - -
379H LEU* 1.3 75.9 - - - +
381H GLY* 1.3 61.1 + - - +
383H LYS* 4.0 23.1 + - - +
384H ASN* 3.4 32.5 + - - +
386H ILE* 3.6 10.0 - - - +
427H PHE* 4.0 17.3 - - + +
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Residues in contact with GLY 381 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296H TYR* 3.1 26.5 - - - +
300H GLY* 3.7 6.5 - - - -
377H ALA 3.1 4.9 + - - -
378H GLY 3.0 6.2 + - - -
380H ASP* 1.3 80.8 - - - +
382H ILE* 1.3 55.8 + - - +
385H LYS 3.0 6.2 + - - -
386H ILE* 2.8 42.4 + - - -
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Residues in contact with ILE 382 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120H ILE* 3.5 38.6 - - + -
274H LEU* 4.1 7.4 - - + -
293H GLN* 3.5 50.0 - - + +
296H TYR* 3.7 12.3 - - + -
297H TYR* 4.0 17.5 - - + +
378H GLY 3.0 14.5 + - - +
379H LEU* 3.6 9.4 - - + +
381H GLY* 1.3 73.3 - - - +
383H LYS* 1.3 68.5 + - - +
384H ASN 3.0 2.8 + - - -
385H LYS* 3.0 31.0 + - - +
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Residues in contact with LYS 383 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H TYR* 3.3 26.8 + - + +
118H THR* 5.0 7.6 - - + -
120H ILE* 4.2 16.2 - - + -
379H LEU* 2.8 22.3 + - + +
380H ASP* 4.0 26.2 + - - +
382H ILE* 1.3 76.2 - - - +
384H ASN* 1.3 73.0 + - - +
385H LYS* 3.9 6.9 + - - +
430H ALA* 4.8 7.7 - - - +
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Residues in contact with ASN 384 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303H LYS* 5.6 3.6 + - - +
380H ASP* 3.4 29.1 + - - +
381H GLY 3.5 0.2 - - - -
382H ILE 3.0 1.0 - - - -
383H LYS* 1.3 104.3 + - - +
385H LYS* 1.3 70.6 + - - +
386H ILE* 2.9 16.3 + - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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