Contacts of the helix formed by residues 294 - 309 (chain B) in PDB entry 5IYB
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 ASP 294 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289B ILE* 4.1 15.6 - - + +
291B ASP* 5.1 6.7 - - + +
292B PHE 3.5 4.6 + - - -
293B GLU* 1.3 77.5 - - - +
295B PRO* 1.3 65.5 - - - +
296B GLU* 3.4 15.8 + - - +
297B MET* 3.1 32.8 + - - +
298B MET* 3.2 18.1 + - - +
377B LEU* 4.3 0.5 - - - +
379B ARG* 2.7 46.7 + - - +
67I GLN* 5.9 3.1 - - - +
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Residues in contact with PRO 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B GLU 3.4 9.4 - - - +
294B ASP* 1.3 90.9 - - - +
296B GLU* 1.3 66.6 + - + +
298B MET* 3.1 13.7 + - + +
299B GLU* 3.1 21.0 + - - +
11I PHE* 3.4 39.9 - - + -
12I VAL* 3.8 14.8 - - - +
13I GLY 4.6 2.8 + - - +
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Residues in contact with GLU 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ASP* 3.1 10.2 - - - +
295B PRO* 1.3 83.6 - - + +
297B MET* 1.3 62.6 + - - +
299B GLU* 3.5 3.1 + - - +
300B MET* 3.1 21.0 + - - +
377B LEU* 5.2 12.2 - - + +
379B ARG* 3.9 16.8 + - - +
11I PHE* 3.5 24.7 - - + -
58I ILE* 5.4 2.5 - - - +
61I GLU* 2.8 35.5 - - - +
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Residues in contact with MET 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ILE* 3.4 32.5 - - + +
289B ILE* 3.2 29.6 - - + -
294B ASP* 3.1 27.5 + - - +
296B GLU* 1.3 78.8 - - - +
298B MET* 1.3 59.0 + - - +
300B MET* 3.1 9.7 + - - +
301B VAL* 2.8 30.6 + - + +
370B HIS* 3.9 20.9 - - - +
373B LEU* 3.3 47.1 - - + -
374B LEU* 4.9 6.5 - - - -
377B LEU* 5.1 1.5 - - - +
379B ARG* 5.5 0.7 - - - -
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Residues in contact with MET 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B LEU* 3.9 29.0 - - + +
289B ILE* 3.7 31.2 - - + -
292B PHE* 3.2 45.5 - - + +
294B ASP 3.2 13.6 + - - +
295B PRO* 3.1 15.7 + - + +
297B MET* 1.3 77.5 - - - +
299B GLU* 1.3 59.5 + - - +
301B VAL* 3.0 25.0 - - + +
302B LYS* 3.1 12.9 + - - +
13I GLY* 4.4 14.4 - - - -
14I ILE* 4.9 17.0 - - + +
16I PHE* 5.7 1.1 - - + -
23I MET* 5.3 1.6 - - - +
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Residues in contact with GLU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1286A ARG* 4.6 10.0 + - - -
295B PRO 3.1 8.5 + - - +
296B GLU 4.0 3.8 - - - +
298B MET* 1.3 73.1 - - - +
300B MET* 1.3 66.3 + - - +
302B LYS* 3.1 53.2 + - + +
303B PRO* 3.2 8.3 - - - +
11I PHE* 3.5 34.8 - - + +
12I VAL 4.6 4.9 - - - +
13I GLY* 3.3 23.6 - - - -
53I ILE 4.3 13.6 - - - +
54I TYR* 4.9 11.8 - - + -
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Residues in contact with MET 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239B MET* 4.3 18.8 - - + -
253B GLY 5.1 6.1 - - - +
254B GLN* 4.0 25.1 - - + +
256B ILE* 5.9 0.7 - - - +
296B GLU 3.1 14.9 + - - +
297B MET* 3.2 11.2 - - - +
299B GLU* 1.3 78.4 - - - +
301B VAL* 1.3 59.0 + - - +
302B LYS 3.6 0.2 + - - -
303B PRO* 3.6 7.5 - - - +
304B SER* 4.9 1.0 + - - -
373B LEU* 3.5 35.4 - - + -
376B ALA* 3.7 34.8 - - + +
377B LEU* 4.1 17.9 - - + -
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B ILE* 6.0 3.4 - - + -
270B ILE* 4.6 12.1 - - + -
285B LEU* 3.8 42.8 - - + -
288B ILE* 4.3 21.1 - - + -
297B MET* 2.8 14.3 + - + +
298B MET* 3.0 25.1 - - - +
300B MET* 1.3 77.0 - - - +
302B LYS* 1.3 64.8 + - - +
303B PRO* 3.5 0.9 - - - -
304B SER* 3.0 23.5 + - - +
305B LEU* 3.4 8.2 + - + +
369B VAL* 5.8 3.6 - - + -
373B LEU* 5.3 7.4 - - + -
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Residues in contact with LYS 302 (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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1286A ARG* 5.9 3.1 - - - +
249B LYS* 5.9 3.6 - - - -
298B MET 3.1 11.7 + - - +
299B GLU* 3.1 50.8 + - - +
301B VAL* 1.3 78.8 - - - +
303B PRO* 1.3 61.2 - - + +
305B LEU* 3.1 7.6 + - - +
306B ASP* 3.0 24.7 + - + +
13I GLY* 4.1 12.0 + - - -
23I MET* 3.3 46.9 - - + +
24I LEU 4.1 9.9 + - - -
25I TYR* 4.0 15.8 - - + +
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Residues in contact with PRO 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LYS* 4.1 21.8 - - + -
254B GLN* 3.3 40.6 - - + +
255B ARG* 5.8 1.8 - - - -
299B GLU 3.2 14.6 - - - +
300B MET 3.6 7.2 - - - +
301B VAL 3.6 3.4 - - - -
302B LYS* 1.3 94.4 - - + +
304B SER* 1.3 56.3 + - - +
306B ASP* 3.3 9.7 + - + +
307B GLU* 3.0 38.2 + - - +
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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
----------------------------------------------------------
254B GLN 3.9 8.5 + - - -
255B ARG* 4.9 1.6 - - - +
256B ILE* 3.0 35.4 + - - +
268B PRO* 5.7 3.7 - - - +
270B ILE* 3.6 28.9 - - - +
301B VAL* 3.0 16.4 + - - -
303B PRO* 1.3 75.6 - - - +
305B LEU* 1.3 64.8 + - - +
307B GLU* 3.4 13.8 + - - +
308B ALA* 3.1 20.3 + - - +
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Residues in contact with LEU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B ILE* 3.9 27.8 - - + -
274B ARG* 5.5 0.5 + - - -
281B ASP* 3.9 36.1 - - + +
284B ILE* 4.8 3.1 - - + -
285B LEU* 3.8 35.4 - - + -
301B VAL* 4.0 14.8 - - + +
302B LYS* 3.1 6.7 + - - +
304B SER* 1.3 76.5 - - - +
306B ASP* 1.3 62.5 + - - +
308B ALA* 3.2 18.1 + - + +
309B PHE* 3.6 16.5 + - + -
23I MET* 3.6 34.8 - - + -
25I TYR* 4.5 2.0 - - - -
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Residues in contact with ASP 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249B LYS* 5.9 3.1 - - - +
302B LYS* 3.0 12.7 + - + +
303B PRO* 3.5 13.5 - - + +
304B SER 3.3 0.2 - - - -
305B LEU* 1.3 77.7 - - - +
307B GLU* 1.3 61.0 + - + +
309B PHE* 3.5 17.2 + - - +
25I TYR* 3.1 26.0 + - - +
40I ARG* 3.0 30.7 + - - -
168S ASN* 5.0 6.1 + - - -
170S VAL* 3.3 33.3 - - + +
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B LYS* 3.5 22.4 + - - +
255B ARG* 3.2 44.3 + - - +
256B ILE 5.2 2.3 - - - +
268B PRO* 4.4 25.8 - - + +
271B ILE* 5.7 3.5 - - - +
303B PRO* 3.0 25.0 + - - +
304B SER* 3.7 12.9 + - - +
305B LEU 3.2 0.2 - - - -
306B ASP* 1.3 75.1 - - + +
308B ALA* 1.3 64.2 + - - +
309B PHE 3.2 1.6 + - - -
310B VAL* 3.9 16.3 + - - +
311B ILE* 5.3 0.5 - - - +
165S GLU* 5.6 2.1 - - - +
168S ASN* 5.2 12.6 + - - +
170S VAL* 5.9 3.1 - - + -
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Residues in contact with ALA 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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268B PRO* 6.3 0.4 - - - +
270B ILE* 3.7 24.5 - - + -
271B ILE* 5.2 4.3 - - - +
274B ARG* 3.4 29.1 + - - +
304B SER 3.1 7.8 + - - +
305B LEU* 3.2 13.3 + - - +
307B GLU* 1.3 77.2 - - - +
309B PHE* 1.3 65.2 + - - +
310B VAL 2.9 2.1 + - - -
311B ILE* 3.0 29.1 + - + +
312B GLN 3.8 2.8 + - - -
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Residues in contact with PHE 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ARG* 4.9 4.5 - - - -
281B ASP* 4.3 18.2 - - - -
305B LEU 3.7 12.3 - - - -
306B ASP* 3.5 17.9 - - - +
307B GLU 3.2 3.4 - - - -
308B ALA* 1.3 77.6 - - - +
310B VAL* 1.3 63.1 + - + +
312B GLN* 3.1 36.4 - - + +
22I ASN* 5.5 4.5 - - + -
23I MET* 4.9 10.8 - - + -
25I TYR* 3.3 28.5 - + - -
40I ARG* 3.3 52.0 - - + -
41I ASN* 5.8 0.2 - - - -
155S LEU* 3.2 19.6 - - - +
177S MET* 6.1 0.7 - - - +
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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
------------------------------------------------------------
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