Contacts of the helix formed by residues 313 - 325 (chain D) in PDB entry 1S77
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 MET 313 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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281D ILE* 5.5 0.2 - - + -
296D LEU* 3.7 21.3 - - + -
297D VAL* 5.5 0.7 - - + -
308D TYR* 4.6 18.6 - - + +
311D VAL* 3.3 19.6 + - + +
312D TYR* 1.3 73.8 - - - +
314D PRO* 1.3 69.2 - - - +
315D GLU 3.2 2.9 - - - -
316D VAL* 2.9 30.7 + - + -
317D TYR* 3.3 37.9 + - + +
731D ASP 5.1 2.5 - - - -
732D GLY* 3.3 20.2 - - - +
733D PHE* 4.0 16.8 - - + -
734D PRO* 4.0 23.3 - - - -
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Residues in contact with PRO 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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312D TYR* 3.4 49.6 - - + +
313D MET* 1.3 89.8 - - - +
315D GLU* 1.3 72.4 + - + +
317D TYR* 3.3 9.5 + - + +
318D LYS* 3.0 30.9 + - + +
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Residues in contact with GLU 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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313D MET 3.2 0.8 - - - -
314D PRO* 1.3 86.7 - - + +
316D VAL* 1.3 60.5 + - - +
318D LYS* 2.8 36.9 + - - +
319D ALA* 3.4 16.8 + - - +
731D ASP* 3.6 31.0 - - + +
792D ARG* 5.1 0.7 - - - +
793D LYS* 5.2 10.8 - - + +
796D VAL* 3.5 23.8 - - + +
800D GLU* 4.0 4.0 - - - +
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Residues in contact with VAL 316 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296D LEU* 5.2 0.9 - - + -
313D MET* 2.9 28.4 + - + +
315D GLU* 1.3 75.8 - - - +
317D TYR* 1.3 64.7 + - - +
318D LYS 3.1 1.3 - - - -
319D ALA* 3.4 3.1 + - - +
320D ILE* 3.3 22.7 + - + +
420D MET* 3.4 37.0 - - + -
731D ASP* 3.6 32.3 - - - +
733D PHE* 3.7 24.9 - - + +
792D ARG* 3.7 13.0 - - - +
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Residues in contact with TYR 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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278D TRP* 3.5 27.6 - - + +
279D THR* 4.1 3.4 - - - -
280D GLY* 3.0 46.0 - - - -
281D ILE* 3.2 11.1 + - - +
296D LEU* 3.3 26.2 - - + +
308D TYR 5.3 0.7 + - - -
311D VAL 4.9 4.9 - - - -
313D MET* 3.3 45.2 + - + +
314D PRO* 3.3 9.3 + - + +
316D VAL* 1.3 78.3 - - - +
318D LYS* 1.3 59.5 + - - +
320D ILE* 3.6 4.0 + - - +
321D ASN* 2.8 42.0 + - - +
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Residues in contact with LYS 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 PRO* 3.0 17.9 + - + +
315D GLU* 2.8 44.7 + - - +
317D TYR* 1.3 76.4 - - - +
319D ALA* 1.3 60.1 + - - +
321D ASN* 3.4 4.8 + - - +
322D ILE* 2.9 48.3 + - + +
796D VAL* 3.4 12.0 - - + +
800D GLU* 3.2 22.9 - - - +
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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
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315D GLU 3.4 9.2 + - - +
316D VAL 3.8 6.7 - - - +
317D TYR 3.3 0.6 - - - -
318D LYS* 1.3 79.1 - - - +
320D ILE* 1.3 56.1 + - + +
322D ILE* 3.1 2.3 + - - +
323D ALA* 2.7 37.5 + - - +
426D VAL* 6.1 0.4 - - + -
792D ARG* 3.5 49.1 - - + +
795D VAL* 3.9 9.3 - - + +
796D VAL* 3.7 7.4 - - + +
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Residues in contact with ILE 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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278D TRP* 3.6 21.5 - - + +
296D LEU* 4.2 9.6 - - + -
316D VAL 3.3 16.7 + - - +
317D TYR* 4.0 5.2 - - - +
319D ALA* 1.3 76.4 - - + +
321D ASN* 1.3 57.6 + - - +
323D ALA* 4.0 3.4 - - + +
324D GLN* 3.0 29.5 + - - +
418D TYR* 3.5 27.2 - - + +
419D ASN 4.5 4.0 - - - +
420D MET* 3.9 30.5 - - + -
426D VAL* 3.5 40.6 - - + -
792D ARG* 4.9 1.8 - - - -
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Residues in contact with ASN 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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277D PRO* 3.3 11.7 - - + +
278D TRP* 2.6 50.9 - - - +
317D TYR* 2.8 29.6 + - - +
318D LYS* 3.8 4.7 - - - +
320D ILE* 1.3 74.8 - - - +
322D ILE* 1.3 66.8 + - + +
324D GLN* 3.1 20.1 + - - +
325D ASN* 3.0 35.3 + - - +
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Residues in contact with ILE 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 LYS* 2.9 42.2 + - + +
319D ALA 3.6 2.9 - - - +
321D ASN* 1.3 75.3 - - + +
323D ALA* 1.3 66.1 + - - +
325D ASN* 3.2 18.4 + - - +
326D THR* 3.8 6.4 + - - -
795D VAL* 3.6 7.0 - - + +
796D VAL* 3.9 30.5 - - + -
799D HIS* 3.9 38.8 - - + +
800D GLU* 5.0 1.3 - - + -
805D GLU 4.4 4.1 - - - +
807D PHE* 3.6 28.9 - - + -
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Residues in contact with ALA 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 2.7 22.1 + - - +
320D ILE* 4.0 4.9 - - - +
322D ILE* 1.3 75.3 - - - +
324D GLN* 1.3 62.5 + - - +
326D THR* 2.8 28.7 + - - -
418D TYR* 3.9 20.6 - - + -
426D VAL* 5.2 4.0 - - + -
795D VAL* 4.1 5.1 - - + +
807D PHE* 4.9 4.7 - - - +
809D LEU* 3.7 29.8 - - + -
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Residues in contact with GLN 324 (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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275D PRO* 2.9 48.8 - - + +
276D LYS 3.3 12.1 + - - -
277D PRO* 3.8 3.6 - - - +
278D TRP* 3.1 24.6 + - - -
285D GLY* 4.1 0.3 - - - -
320D ILE 3.0 13.1 + - - +
321D ASN* 3.1 33.2 + - - +
323D ALA* 1.3 78.3 - - - +
325D ASN* 1.3 59.6 + - - +
326D THR 3.1 5.2 + - - +
415D TRP* 3.6 6.1 - - - +
416D PHE 3.4 6.4 + - - +
417D PRO* 3.5 4.7 - - - +
418D TYR* 2.9 46.9 + - + +
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Residues in contact with ASN 325 (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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274D PRO* 3.3 30.5 - - - +
275D PRO* 4.0 12.1 + - - +
277D PRO* 5.5 7.8 - - - +
321D ASN* 3.0 28.8 + - - +
322D ILE* 3.2 9.4 + - - +
323D ALA 3.1 1.4 + - - -
324D GLN* 1.3 78.0 + - - +
326D THR* 1.3 62.1 + - - +
327D ALA* 3.4 3.5 + - - +
415D TRP* 3.5 11.7 + - - -
805D GLU* 4.9 3.3 - - - +
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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