Contacts of the helix formed by residues 308 - 323 (chain D) in PDB entry 1XFV
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 308 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307D LEU* 1.3 72.8 - - - +
309D PRO* 1.3 61.1 - - + +
310D GLU* 3.8 10.8 - - + +
311D HIS* 2.6 75.9 + - + +
312D ALA 2.9 5.2 + - - -
336D THR* 2.8 38.4 - - + +
339D ILE* 3.9 3.1 - - + -
340D LYS* 3.7 29.6 - - + +
492D TYR* 3.1 11.2 + - - +
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Residues in contact with PRO 309 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299D GLU* 5.3 7.4 - - + +
302D LEU* 4.3 31.2 - - + +
307D LEU 3.3 9.4 - - - +
308D VAL* 1.3 84.3 - - + -
310D GLU* 1.3 66.4 + - + +
311D HIS 2.8 1.7 + - - -
312D ALA* 3.0 11.8 + - - +
313D ASP* 2.8 24.0 + - - +
336D THR* 4.4 6.5 - - + -
340D LYS* 5.6 8.5 - - - +
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Residues in contact with GLU 310 (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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308D VAL* 3.4 7.4 - - + +
309D PRO* 1.3 80.6 - - + +
311D HIS* 1.3 55.9 + - + +
313D ASP* 4.0 8.3 - - - +
314D ALA* 3.1 25.5 + - - +
340D LYS* 2.9 38.1 + - + +
567D THR* 3.4 31.8 + - + +
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Residues in contact with HIS 311 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307D LEU* 5.3 0.4 - - + -
308D VAL* 2.6 49.4 + - + +
310D GLU* 1.3 71.1 - - + +
312D ALA* 1.3 65.8 + - - +
314D ALA* 2.8 7.7 + - - +
315D PHE* 2.7 27.6 + - + -
339D ILE* 3.6 19.1 - - + -
340D LYS* 4.6 5.2 - - - -
492D TYR* 2.7 26.1 + + + +
564D VAL* 3.1 38.3 - - + +
567D THR* 3.6 18.0 - - + +
569D TYR* 4.0 17.9 - + - -
574D VAL* 5.1 1.3 - - + -
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Residues in contact with ALA 312 (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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302D LEU* 3.5 30.1 - - + -
307D LEU* 4.6 8.4 - - + +
308D VAL 2.9 8.0 + - - +
309D PRO 3.5 6.5 - - - +
311D HIS* 1.3 72.8 - - - +
313D ASP* 1.3 52.6 + - - +
315D PHE* 2.7 37.3 + - - +
316D LYS* 2.8 15.2 + - - +
594D PHE* 4.6 5.8 - - + -
596D ILE* 4.2 5.4 - - + +
602D PHE* 3.6 17.7 - - + -
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Residues in contact with ASP 313 (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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302D LEU* 5.0 3.6 - - - +
309D PRO* 2.8 26.0 + - - +
310D GLU* 3.9 8.2 + - - +
312D ALA* 1.3 77.8 - - - +
314D ALA* 1.3 58.0 + - - +
316D LYS* 2.7 59.0 + - - +
317D LYS* 3.5 2.8 + - - +
602D PHE* 3.8 15.8 - - - -
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Residues in contact with ALA 314 (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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310D GLU 3.1 16.7 + - - +
311D HIS* 2.8 19.7 + - - +
313D ASP* 1.3 75.6 - - - +
315D PHE* 1.3 60.5 + - - +
317D LYS* 3.5 12.3 + - - +
318D ILE* 3.2 17.4 - - - +
563D ALA* 4.4 9.8 - - - +
564D VAL* 4.3 10.8 - - + -
567D THR* 4.1 18.2 - - - +
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Residues in contact with PHE 315 (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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307D LEU* 3.8 14.4 - - + -
311D HIS 2.7 16.4 + - - -
312D ALA* 2.7 24.7 + - - +
314D ALA* 1.3 69.5 - - - +
316D LYS* 1.3 64.4 + - - +
317D LYS 2.7 5.0 + - - -
318D ILE* 2.8 19.7 + - + +
319D ALA* 3.2 10.6 + - - +
326D ILE* 4.8 4.2 - - + +
328D PHE* 3.4 32.5 - + - -
492D TYR* 4.0 22.9 - + - -
560D LEU* 3.5 47.3 - - + -
563D ALA* 4.9 0.2 - - + -
564D VAL* 3.5 28.7 - - + -
574D VAL* 4.2 4.5 - - + -
575D VAL* 4.6 1.3 - - + -
596D ILE* 3.8 14.1 - - + -
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Residues in contact with LYS 316 (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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312D ALA 2.8 7.1 + - - +
313D ASP* 2.7 43.6 + - - +
315D PHE* 1.3 74.8 - - - +
317D LYS* 1.3 60.1 + - - +
319D ALA* 3.9 2.8 + - - +
320D ARG* 3.6 25.4 + - - +
596D ILE* 4.5 11.4 - - + +
600D GLY* 3.3 35.0 - - - +
602D PHE* 3.9 17.9 - - + -
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Residues in contact with LYS 317 (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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313D ASP 3.5 2.1 + - - +
314D ALA* 3.5 13.8 + - - +
315D PHE 2.7 4.6 + - - -
316D LYS* 1.3 74.7 - - - +
318D ILE* 1.3 64.7 + - + +
320D ARG* 3.4 8.4 + - - +
321D GLU* 2.9 30.7 + - + +
559D ARG* 5.3 8.5 - - - +
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Residues in contact with ILE 318 (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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314D ALA 3.2 23.1 - - - +
315D PHE* 2.8 18.5 + - - +
317D LYS* 1.3 75.4 - - + +
319D ALA* 1.3 70.2 + - - +
321D GLU* 4.4 5.6 - - - +
322D LEU* 2.9 49.4 + - + +
324D THR* 5.7 0.2 - - - -
326D ILE* 5.4 0.4 - - + -
556D MET* 4.3 15.7 - - - -
559D ARG* 3.7 39.0 - - + +
560D LEU* 4.4 11.4 - - + -
563D ALA* 3.5 21.5 - - + -
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Residues in contact with ALA 319 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315D PHE 3.2 5.3 + - - +
316D LYS 3.9 7.4 - - - +
318D ILE* 1.3 75.8 - - - +
320D ARG* 1.3 54.2 + - + +
323D ASN* 2.6 38.1 + - - -
324D THR* 3.0 25.4 + - - +
326D ILE* 4.6 9.4 - - + +
596D ILE* 3.8 21.1 - - + +
597D ASN 3.4 24.5 - - - +
598D PRO* 4.2 2.5 - - - -
600D GLY* 5.5 0.2 - - - -
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Residues in contact with ARG 320 (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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316D LYS* 3.6 13.4 + - - +
317D LYS* 3.4 10.3 + - - +
318D ILE 3.1 0.2 - - - -
319D ALA* 1.3 75.8 - - - +
321D GLU* 1.3 70.2 + - - +
323D ASN* 2.7 17.8 + - - +
598D PRO 3.0 22.6 + - - +
599D GLU* 2.9 37.1 + - - +
600D GLY* 5.1 0.9 - - - -
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Residues in contact with GLU 321 (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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317D LYS* 2.9 21.4 + - + +
318D ILE* 4.0 4.0 - - - +
320D ARG* 1.3 79.1 - - - +
322D LEU* 1.3 66.1 + - + +
323D ASN* 3.3 3.5 + - - +
503D GLU* 4.1 3.1 - - - +
506D LYS* 5.3 2.9 + - - -
559D ARG* 2.6 46.6 + - - +
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Residues in contact with LEU 322 (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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318D ILE* 2.9 39.7 + - + +
319D ALA 3.5 0.2 - - - -
321D GLU* 1.3 81.1 - - + +
323D ASN* 1.3 68.8 + - - +
324D THR* 2.9 18.1 - - + +
503D GLU* 2.4 50.2 - - + +
555D GLN* 4.6 18.6 - - - +
556D MET* 3.6 20.4 - - + -
559D ARG* 3.7 27.1 - - + +
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Residues in contact with ASN 323 (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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319D ALA 2.6 16.4 + - - -
320D ARG* 2.7 15.7 + - - +
321D GLU 4.5 2.2 - - - +
322D LEU* 1.3 77.0 - - - +
324D THR* 1.3 60.5 + - - +
500D SER* 3.3 29.1 + - - -
502D THR* 4.7 4.6 + - - +
503D GLU* 4.2 4.5 - - - +
598D PRO* 3.2 12.9 - - - +
624D TYR* 2.3 33.6 + - - -
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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