Contacts of the helix formed by residues 348 - 360 (chain B) in PDB entry 6WCZ
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 348 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315B GLN 5.1 0.2 - - - -
316B GLY 4.8 4.0 - - - +
317B SER* 3.9 7.9 - - - +
318B ALA* 3.4 38.4 - - + +
346B ASP* 3.7 9.6 + - - +
347B THR* 1.3 79.4 - - - +
349B PRO* 1.3 70.1 - - - +
350B TYR* 4.0 10.9 + - - +
351B GLY* 2.9 28.4 + - - -
352B GLN* 3.0 12.1 + - - +
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Residues in contact with PRO 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B GLN 4.4 13.0 - - - +
347B THR 4.5 0.9 - - - +
348B THR* 1.3 83.9 - - - +
350B TYR* 1.3 60.0 + - - +
352B GLN* 4.0 8.6 - - + +
353B GLN* 3.0 23.9 + - - +
582B LEU* 4.0 33.2 - - + +
583B ARG 4.1 1.8 - - - +
584B PRO* 3.2 37.1 - - + +
590B THR* 4.2 21.5 - - + +
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Residues in contact with TYR 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B GLY 6.0 1.6 - - - -
49B ALA* 3.7 27.1 - - + -
115B LEU 2.4 29.8 + - - -
117B GLN* 3.8 28.2 - - + +
121B TRP* 4.9 2.0 - + - -
346B ASP* 5.1 4.0 - - - -
348B THR* 3.2 9.8 - - - +
349B PRO* 1.3 79.8 - - - +
351B GLY* 1.3 62.0 + - - +
353B GLN* 3.8 1.4 - - - +
354B ARG* 2.9 68.9 + - + +
459B ARG* 5.8 0.2 - - - -
465B GLU* 3.4 21.1 + - + +
584B PRO* 3.8 15.3 - - + +
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Residues in contact with GLY 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346B ASP* 3.3 28.9 - - - -
348B THR* 2.9 12.0 + - - -
350B TYR* 1.3 82.3 - - - +
352B GLN* 1.3 62.2 + - - +
355B VAL* 3.0 10.6 + - - +
457B GLY 4.4 6.3 - - - -
459B ARG* 2.4 27.7 + - - -
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Residues in contact with GLN 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B THR* 3.1 22.2 + - - +
348B THR 3.0 16.1 + - - +
349B PRO* 4.0 4.0 - - - +
351B GLY* 1.3 75.0 - - - +
353B GLN* 1.3 57.9 + - - +
355B VAL* 4.4 1.2 - - - +
356B PHE* 3.0 30.7 + - - +
454B ASN* 5.2 1.4 + - - +
455B MET* 3.9 32.0 + - + +
456B MET* 4.2 7.5 - - - +
457B GLY* 3.9 24.9 - - - +
581B VAL* 4.9 0.2 - - - -
582B LEU* 3.2 52.1 + - - +
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Residues in contact with GLN 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B GLN* 4.0 23.8 - - - +
121B TRP* 4.7 7.0 + - + -
263B THR* 5.4 0.4 + - - -
300B PRO* 3.4 29.3 - - - +
301B TYR* 4.5 6.8 + - - -
349B PRO 3.0 19.5 + - - +
350B TYR 3.8 2.9 - - - +
352B GLN* 1.3 77.7 - - - +
354B ARG* 1.3 58.8 + - - +
356B PHE* 3.4 23.3 - - - +
357B LYS* 3.0 30.6 + - - +
581B VAL* 5.8 1.6 - - - +
582B LEU 3.8 5.5 + - - +
583B ARG* 3.6 28.4 - - + +
584B PRO* 4.0 10.1 - - + -
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Residues in contact with ARG 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 3.9 20.9 - - - +
117B GLN* 6.0 0.2 - - - +
121B TRP* 3.6 39.3 - - + +
346B ASP* 5.6 0.4 + - - -
350B TYR* 2.9 52.6 + - + +
352B GLN 3.2 0.2 - - - -
353B GLN* 1.3 74.1 - - - +
355B VAL* 1.3 61.0 + - - +
356B PHE 3.2 0.9 - - - -
357B LYS* 3.3 2.1 + - - +
358B GLU* 3.0 64.6 + - + +
459B ARG* 3.0 27.8 - - - +
461B LYS* 3.1 31.1 - - - +
465B GLU* 4.3 5.5 - - - +
468B LYS 3.6 13.1 + - - +
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Residues in contact with VAL 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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351B GLY 3.0 13.6 + - - +
352B GLN 4.4 1.8 - - - +
354B ARG* 1.3 73.1 - - - +
356B PHE* 1.3 64.5 + - - +
358B GLU* 3.8 6.5 - - - +
359B LYS* 3.1 22.9 + - - +
360B VAL* 4.0 3.4 + - + +
457B GLY* 4.4 16.4 - - - -
459B ARG* 3.0 46.9 - - + +
470B LYS* 4.3 25.7 - - + +
472B SER 5.0 0.9 - - - +
474B ALA* 3.9 29.8 - - + +
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Residues in contact with PHE 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B PRO 4.1 8.5 - - - -
301B TYR* 3.5 35.4 - + - -
304B TRP* 3.6 44.6 - + - -
352B GLN 3.0 21.9 + - - +
353B GLN* 3.4 23.1 - - - +
355B VAL* 1.3 77.3 - - - +
357B LYS* 1.3 66.0 + - + +
360B VAL* 3.0 48.2 + - + +
361B ASP* 3.4 15.4 + - + -
455B MET* 5.1 14.6 - - + -
581B VAL* 5.4 8.7 - - + -
595B ILE* 5.3 2.5 - - + -
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Residues in contact with LYS 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 5.3 6.3 - - - +
121B TRP* 3.8 45.3 - - + +
122B ASN* 4.6 24.0 - - + +
124B VAL* 4.3 20.2 + - - +
125B ARG* 5.1 11.8 - - - +
302B ARG* 5.9 1.4 + - - -
353B GLN* 3.0 21.3 + - - +
354B ARG 3.3 2.4 + - - +
356B PHE* 1.3 83.2 - - + +
358B GLU* 1.3 83.2 + - - +
360B VAL 4.7 0.7 + - - -
361B ASP* 4.8 11.7 + - - +
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Residues in contact with GLU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B LEU* 5.1 3.8 - - - +
125B ARG* 6.1 2.5 - - - +
354B ARG* 3.0 55.3 + - - +
355B VAL* 3.8 10.0 - - - +
356B PHE 3.3 0.4 - - - -
357B LYS* 1.3 100.0 + - - +
359B LYS* 1.3 68.7 + - + +
362B THR* 4.9 3.6 + - - -
459B ARG* 4.4 0.7 + - - -
468B LYS 3.6 7.4 - - - +
469B ALA* 3.3 38.9 - - + +
470B LYS* 4.0 2.5 + - + -
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Residues in contact with LYS 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B VAL 3.1 6.0 + - - -
358B GLU* 1.3 88.0 - - + +
360B VAL* 1.3 58.6 + - - +
362B THR* 4.5 8.5 - - - +
469B ALA* 4.3 26.3 + - + +
470B LYS* 2.6 51.6 + - + +
537B ALA* 5.4 9.9 - - - +
538B GLY* 5.6 9.4 - - - +
541B THR* 3.6 17.1 - - + +
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303B THR* 4.6 0.2 + - - -
304B TRP* 3.4 38.4 + - + +
355B VAL 4.2 1.1 - - - +
356B PHE* 3.0 38.2 + - + +
358B GLU 3.9 0.4 - - - -
359B LYS* 1.3 82.7 - - - +
361B ASP* 1.3 56.7 + - - +
362B THR* 2.7 19.4 + - - -
455B MET* 6.1 1.6 - - + -
470B LYS* 3.7 13.0 - - - +
474B ALA* 4.5 13.9 - - + -
476B TRP* 4.7 12.3 - - + -
541B THR* 5.4 0.9 - - + -
597B ARG* 5.5 1.7 + - - -
600B GLN* 3.8 25.4 + - - +
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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