Contacts of the helix formed by residues 300 - 313 (chain B) in PDB entry 1WBB
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 300 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ARG* 5.8 1.8 - - - -
298B THR* 4.1 2.8 + - - -
299B VAL* 1.3 80.8 - - + +
301B PRO* 1.3 67.0 - - - +
302B MET* 3.3 15.4 - - + +
303B GLY* 3.1 12.3 + - - -
304B SER* 3.3 13.5 + - - -
342B LEU* 3.3 31.4 - - + +
345B VAL* 4.7 1.8 - - + -
346B GLY* 3.5 29.4 - - - +
549B LEU 5.4 0.2 - - - +
553B ASP* 2.7 32.9 + - + +
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Residues in contact with PRO 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLU* 3.4 53.3 - - + +
128B ARG* 4.4 8.5 - - + +
299B VAL 4.4 2.9 - - - +
300B THR* 1.3 87.9 - - - +
302B MET* 1.3 60.7 + - - +
304B SER* 3.4 8.9 + - - -
305B ARG* 3.2 30.3 + - - +
346B GLY* 4.3 3.1 - - - -
347B ASP* 4.0 30.1 - - + +
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Residues in contact with MET 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300B THR* 3.3 14.4 - - + +
301B PRO* 1.3 79.1 - - - +
303B GLY* 1.3 60.6 + - - +
305B ARG* 3.5 27.9 + - - +
306B MET* 3.2 21.0 + - - +
309B ARG* 5.0 2.3 + - - -
345B VAL* 3.7 13.2 - - + -
346B GLY 3.6 21.3 - - - +
347B ASP* 3.8 7.7 + - - +
348B LEU* 4.0 8.5 - - + -
349B GLU* 3.6 33.0 - - + +
546B ALA* 3.3 28.3 - - - +
549B LEU* 3.6 23.8 - - + -
550B ALA* 4.0 14.1 - - + +
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Residues in contact with GLY 303 (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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298B THR* 3.8 7.5 - - - +
300B THR* 3.1 11.3 + - - -
302B MET* 1.3 74.8 - - - +
304B SER* 1.3 59.3 + - - +
305B ARG 3.3 0.2 - - - -
306B MET* 3.4 0.6 + - - -
307B LEU* 3.0 25.1 + - - +
550B ALA* 3.7 22.4 - - - -
553B ASP* 3.6 13.9 - - - -
554B VAL* 3.2 12.7 - - - +
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Residues in contact with SER 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B ARG* 3.4 28.9 + - - +
296B ASP* 2.4 26.2 + - - +
298B THR* 3.1 20.9 + - - -
300B THR 3.3 10.3 + - - -
301B PRO 3.6 9.0 - - - -
303B GLY* 1.3 76.0 - - - +
305B ARG* 1.3 62.4 + - - +
307B LEU* 3.4 3.6 + - - +
308B LYS* 3.2 36.5 + - - +
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Residues in contact with ARG 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B GLU 3.0 19.4 + - - -
128B ARG 3.6 22.2 - - - +
129B GLN 3.8 7.9 - - - +
130B ASP* 3.3 29.5 + - - +
149B ASP* 5.2 1.0 + - - -
301B PRO 3.2 17.6 + - - +
302B MET* 3.5 15.8 - - - +
304B SER* 1.3 79.6 - - - +
306B MET* 1.3 62.8 + - - +
308B LYS* 3.4 8.1 + - - +
309B ARG* 3.2 30.8 + - - +
347B ASP* 3.0 39.0 + - - -
349B GLU* 2.5 34.1 + - - -
350B ARG* 3.6 33.1 - - - +
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Residues in contact with MET 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B MET 3.2 14.6 + - - +
303B GLY* 3.7 5.6 - - - +
304B SER 3.2 0.6 - - - -
305B ARG* 1.3 75.5 - - - +
307B LEU* 1.3 59.4 + - - +
309B ARG* 3.3 31.1 + - - +
310B TRP* 3.0 61.2 + - + +
349B GLU* 5.4 3.8 - - - +
547B SER* 3.8 18.8 - - - +
550B ALA* 3.7 21.3 - - + -
551B GLU* 3.6 29.8 - - + +
554B VAL* 3.9 8.3 - - + -
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Residues in contact with LEU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU* 4.0 6.5 - - + +
296B ASP* 3.4 47.1 - - + +
298B THR* 4.7 1.1 - - + -
303B GLY 3.0 16.9 + - - +
304B SER* 3.7 5.2 - - - +
305B ARG 3.4 0.2 - - - -
306B MET* 1.3 74.6 - - - +
308B LYS* 1.3 60.2 + - + +
310B TRP* 3.2 5.6 + - + +
311B LEU* 2.9 43.9 + - + +
554B VAL* 3.8 25.7 - - + +
557B ASN* 3.8 11.2 - - - +
558B LEU* 4.0 22.7 - - + -
636B ILE* 4.2 15.5 - - + -
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Residues in contact with LYS 308 (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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128B ARG* 2.7 38.9 + - - +
129B GLN* 4.6 9.0 - - + +
280B THR* 3.7 29.9 - - + +
292B ALA* 4.8 11.2 - - + -
296B ASP* 4.0 9.6 - - - +
304B SER* 3.2 28.3 + - - +
305B ARG* 3.8 8.5 - - - +
306B MET 3.3 0.2 - - - -
307B LEU* 1.3 78.4 - - + +
309B ARG* 1.3 61.3 + - - +
311B LEU* 3.6 8.6 + - + +
312B HIS* 3.3 31.6 + - + -
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Residues in contact with ARG 309 (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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130B ASP* 3.0 39.6 + - - +
132B LEU* 6.6 0.2 - - - -
149B ASP* 5.2 3.2 + - - -
154B ARG* 3.6 50.4 - - - +
172B ARG* 5.6 1.4 + - - +
302B MET 5.0 1.6 + - - -
305B ARG* 3.2 23.3 + - - +
306B MET* 3.5 48.0 - - - +
307B LEU 3.1 0.2 - - - -
308B LYS* 1.3 76.0 - - + +
310B TRP* 1.3 69.9 + - + +
312B HIS* 3.2 6.3 + - - +
313B MET* 3.1 31.1 + - + +
349B GLU* 4.8 12.1 + - - -
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Residues in contact with TRP 310 (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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306B MET* 3.0 43.9 + - + +
307B LEU* 3.2 8.7 + - - +
309B ARG* 1.3 81.7 - - + +
311B LEU* 1.3 62.3 + - - +
313B MET* 3.3 27.8 + - + +
314B PRO* 3.6 1.4 - - - +
324B ARG* 3.5 54.5 + - + +
551B GLU* 4.1 30.3 - - + -
554B VAL* 3.5 27.6 - - + -
555B LEU* 3.7 25.1 - - + -
558B LEU* 4.3 8.7 - - + -
636B ILE* 3.5 29.0 - - + +
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Residues in contact with LEU 311 (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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269B MET* 4.1 0.9 - - - +
279B ILE* 3.6 22.7 - - + +
280B THR* 5.3 0.7 - - + -
291B LEU* 3.8 28.9 - - + -
292B ALA* 4.4 24.5 - - + -
295B LEU* 4.0 16.4 - - + -
307B LEU* 2.9 35.0 + - + +
308B LYS* 4.0 10.8 - - - +
309B ARG 3.3 0.2 - - - -
310B TRP* 1.3 76.0 - - - +
312B HIS* 1.3 61.7 + - - +
313B MET 3.4 0.7 + - - -
314B PRO* 3.6 6.2 - - - +
632B LEU* 3.6 30.4 - - + +
633B MET* 5.5 0.4 - - + -
636B ILE* 3.3 26.0 - - + -
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Residues in contact with HIS 312 (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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172B ARG* 3.4 31.7 - - + +
267B ILE 5.3 0.7 - - - +
269B MET* 4.0 0.8 - - - +
274B ARG* 2.9 58.2 + - + +
279B ILE* 3.6 24.7 - - + +
280B THR* 2.5 38.1 + - + +
308B LYS* 3.3 22.1 + - + +
309B ARG* 3.2 6.2 + - - +
311B LEU* 1.3 75.6 - - - +
313B MET* 1.3 58.3 + - - +
314B PRO* 3.5 6.2 - - - +
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Residues in contact with MET 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154B ARG* 3.9 26.7 - - - +
156B ARG* 5.4 3.6 - - - +
172B ARG* 4.0 24.5 - - - +
261B GLU* 3.8 30.1 - - - +
266B SER* 4.1 21.8 - - - +
267B ILE 5.6 0.4 - - - -
309B ARG* 3.1 19.1 + - + +
310B TRP* 3.3 17.3 - - + +
311B LEU 3.2 0.2 - - - -
312B HIS* 1.3 79.4 - - - +
314B PRO* 1.3 67.7 - - - +
315B VAL* 3.4 6.6 + - - +
324B ARG* 5.7 0.9 + - - -
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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