Contacts of the helix formed by residues 422 - 434 (chain D) in PDB entry 3IFS
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 VAL 422 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311C LEU 3.9 20.6 - - - +
312C HIS* 5.6 0.9 - - - +
315C GLY 4.5 1.6 - - - -
316C GLN* 3.9 19.5 + - + +
291D GLU* 4.3 14.1 - - - +
419D GLN* 3.3 26.5 - - + +
421D GLY* 1.3 75.2 - - - +
423D GLU* 1.3 75.7 + - - +
424D ALA 3.3 0.2 - - - -
425D TYR* 3.2 22.9 - - + -
426D LYS* 3.1 39.0 - - - +
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Residues in contact with GLU 423 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419D GLN 4.9 1.2 - - - +
420D PRO* 3.6 20.6 - - + +
421D GLY 3.2 1.2 - - - -
422D VAL* 1.3 89.7 - - + +
424D ALA* 1.3 59.5 + - - +
426D LYS* 3.4 20.7 + - - +
427D LYS* 2.9 33.7 + - - +
430D PHE* 5.9 1.4 - - - -
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Residues in contact with ALA 424 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C GLN* 3.8 33.2 - - + +
373C ALA* 3.8 8.1 - - + -
420D PRO 4.7 0.6 + - - -
421D GLY* 3.6 5.6 + - - +
422D VAL 3.3 1.0 - - - -
423D GLU* 1.3 78.4 - - - +
425D TYR* 1.3 63.8 + - - +
427D LYS* 3.5 8.4 + - - +
428D ASN* 3.2 27.6 + - - +
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Residues in contact with TYR 425 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C SER* 5.6 0.9 - - - -
311C LEU* 3.7 38.8 - - + +
312C HIS* 3.3 34.3 + - - -
315C GLY* 5.7 2.5 - - - -
319C GLN* 4.7 1.9 + - - +
366C ALA* 6.0 0.7 - - + -
369C GLY 4.3 3.8 - - - -
370C THR* 3.4 37.9 - - + +
373C ALA* 3.7 12.0 - - + +
374C HIS* 5.1 4.5 - - - +
151D GLU* 4.2 4.9 + - - -
421D GLY 4.8 0.9 + - - -
422D VAL* 3.2 39.7 - - + -
423D GLU 3.5 0.2 - - - -
424D ALA* 1.3 78.3 - - - +
426D LYS* 1.3 79.0 + - + +
428D ASN* 3.4 1.4 + - - +
429D MSE 2.8 52.4 + - + +
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Residues in contact with LYS 426 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C HIS* 4.9 11.2 + - - -
149D THR* 5.2 10.9 + - - +
422D VAL* 3.1 37.5 - - - +
423D GLU* 3.4 25.5 + - - +
424D ALA 3.3 0.6 - - - -
425D TYR* 1.3 107.4 - - + +
427D LYS* 1.3 57.5 + - - +
429D MSE 3.3 10.2 + - + +
430D PHE* 2.9 56.3 + - + -
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Residues in contact with LYS 427 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423D GLU* 2.9 17.9 + - + +
424D ALA* 3.9 7.2 - - - +
426D LYS* 1.3 76.8 - - - +
428D ASN* 1.3 68.4 + - - +
430D PHE* 3.3 11.1 + - - +
431D ALA* 3.0 23.4 + - - +
438D PHE* 3.9 17.9 - - + -
441D LEU* 3.3 30.7 - - + +
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Residues in contact with ASN 428 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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369C GLY* 3.1 35.3 + - - +
372C LEU* 3.9 9.7 - - - +
373C ALA* 3.3 25.3 - - - +
376C ASP* 4.9 4.0 + - - -
424D ALA* 3.2 11.8 + - - +
425D TYR 3.8 0.2 - - - +
427D LYS* 1.3 84.1 - - - +
429D MSE 1.3 62.8 + - - +
431D ALA* 3.4 2.4 + - - +
432D LEU* 3.0 28.4 + - - +
441D LEU* 3.8 12.8 - - - +
445D LEU* 3.6 29.2 - - + +
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Residues in contact with MSE 429 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308C SER* 6.4 0.7 - - - -
362C VAL* 5.0 1.8 - - - +
365C LYS 4.1 13.0 - - - +
366C ALA* 3.8 37.9 - - - +
369C GLY* 4.1 2.0 - - - -
121D ILE* 4.8 5.8 - - - -
150D THR* 3.4 34.3 - - - +
151D GLU* 5.6 4.7 - - - +
425D TYR* 2.8 35.6 + - + +
426D LYS* 3.6 13.5 - - + +
428D ASN* 1.3 77.1 - - - +
430D PHE* 1.3 81.6 + - + +
432D LEU* 3.1 3.6 + - - +
433D LEU* 2.9 44.2 + - + +
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Residues in contact with PHE 430 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C TYR* 4.8 1.1 - - - -
148D THR 5.6 4.9 - - - -
150D THR* 3.7 23.3 - - - -
423D GLU* 5.9 0.9 - - - -
426D LYS* 2.9 45.1 + - + +
427D LYS* 3.7 6.3 - - - +
429D MSE 1.3 86.8 - - + +
431D ALA* 1.3 63.5 + - - +
433D LEU* 3.2 17.2 + - + +
435D LYS* 2.9 68.1 + - + +
438D PHE* 3.9 21.5 - + + -
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Residues in contact with ALA 431 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427D LYS 3.0 16.4 + - - +
428D ASN 3.5 4.9 - - - +
430D PHE* 1.3 76.7 - - - +
432D LEU* 1.3 57.1 + - - +
434D GLY* 3.1 16.5 + - - -
435D LYS 4.2 0.2 + - - -
438D PHE* 3.6 20.6 - - + +
441D LEU* 3.7 15.7 - - + -
442D LYS* 3.1 47.3 - - - +
445D LEU* 4.2 1.8 - - + -
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Residues in contact with LEU 432 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361C PHE* 4.4 3.1 - - - -
365C LYS* 3.8 31.7 - - + +
368C GLU* 3.7 19.3 - - + +
369C GLY* 3.5 35.7 - - - +
372C LEU* 4.7 0.9 - - + -
428D ASN 3.0 15.1 + - - +
429D MSE 3.8 3.4 - - - +
431D ALA* 1.3 76.6 - - - +
433D LEU* 1.3 60.3 + - - +
434D GLY 3.2 0.6 + - - -
442D LYS* 4.2 16.2 + - + +
445D LEU* 3.9 29.2 - - + -
446D GLU* 3.9 32.3 - - + +
449D LEU* 3.9 14.1 - - + -
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Residues in contact with LEU 433 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C TYR* 3.4 36.1 - - + +
354C LEU* 3.8 15.9 - - + +
361C PHE* 3.9 20.4 - - + -
362C VAL* 3.6 36.6 - - + +
365C LYS* 3.5 26.9 - - + -
150D THR* 5.3 4.3 - - + -
429D MSE 2.9 42.2 + - + +
430D PHE* 3.2 10.3 + - + +
432D LEU* 1.3 76.9 - - - +
434D GLY* 1.3 58.2 - - - +
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Residues in contact with GLY 434 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353C TYR* 3.6 12.4 - - - +
431D ALA 3.1 13.5 + - - -
432D LEU 3.2 1.0 - - - -
433D LEU* 1.3 80.6 - - - +
435D LYS* 1.3 66.4 + - - +
436D PRO* 3.5 3.6 - - - +
439D GLU* 5.3 1.8 - - - +
442D LYS* 4.3 15.3 - - - -
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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
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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