Contacts of the helix formed by residues 303 - 318 (chain B) in PDB entry 5FQD
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 SER 303 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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927A MET* 3.4 16.1 - - - +
951A PRO* 3.9 17.3 - - - +
188B CYS* 3.7 12.4 + - - -
190B LEU* 4.6 4.5 + - - +
301B ILE* 3.2 8.3 - - - +
302B GLY* 1.4 77.7 - - - +
304B ALA* 1.3 65.2 + - - +
305B ILE* 3.4 14.7 + - - +
306B GLN* 3.1 24.9 + - - -
307B ARG* 3.0 20.6 + - - +
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Residues in contact with ALA 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLU* 3.8 5.9 + - - -
188B CYS 4.0 5.7 + - - +
277B PRO* 3.9 38.6 - - + +
278B ILE* 3.9 13.2 - - + +
281B SER* 4.1 0.9 - - - +
303B SER* 1.3 71.5 + - - +
305B ILE* 1.4 58.0 + - + +
307B ARG* 3.2 19.0 + - - +
308B LEU* 2.8 37.5 + - + +
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Residues in contact with ILE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
927A MET* 3.8 20.6 - - + -
953A TRP* 4.3 15.0 - - + -
190B LEU* 5.2 9.0 - - + +
248B TYR* 3.4 35.2 - - + +
250B ALA* 3.6 40.4 - - + +
253B LEU* 3.9 5.1 - - + +
277B PRO* 5.6 0.7 - - + -
303B SER* 3.2 11.5 - - - +
304B ALA* 1.4 79.3 - - + +
306B GLN* 1.3 56.7 + - - +
308B LEU* 3.5 6.3 + - + +
309B ARG* 3.0 38.3 + - - +
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Residues in contact with GLN 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
909A ILE* 6.2 0.4 - - - +
927A MET* 3.8 26.5 + - + +
929A SER* 3.9 19.4 + - - -
949A PHE* 5.1 9.3 - - - +
951A PRO* 3.7 18.8 - - - +
301B ILE* 3.7 13.3 - - + +
302B GLY 4.8 1.7 + - - -
303B SER* 3.1 28.8 + - - +
305B ILE* 1.3 76.0 - - - +
307B ARG* 1.4 56.4 + - - +
309B ARG* 3.6 1.2 + - - +
310B CYS* 3.0 30.8 + - - +
436B ASP* 3.3 45.7 + - + +
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Residues in contact with ARG 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187B GLU* 3.0 30.9 + - - -
278B ILE 4.3 0.8 + - - -
281B SER* 2.8 41.1 + - - -
282B TYR* 3.2 42.4 + - - -
285B ALA* 4.8 3.6 - - - -
298B LEU* 4.0 19.9 + - + +
301B ILE* 2.8 41.6 + - + +
302B GLY* 3.5 11.9 - - - -
303B SER 3.0 8.1 + - - +
304B ALA* 3.5 18.4 - - - +
306B GLN* 1.4 73.2 - - - +
308B LEU* 1.4 59.1 + - - +
310B CYS* 3.3 3.6 + - - +
311B GLU* 3.0 47.3 + - - +
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Residues in contact with LEU 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ALA* 4.0 32.1 - - + +
253B LEU* 4.1 12.1 - - + -
254B MET* 3.9 9.6 - - + -
257B ILE* 3.6 22.8 - - + +
277B PRO* 4.3 12.8 - - + +
280B PHE* 3.5 32.1 - - + -
281B SER* 3.8 18.8 - - - +
304B ALA 2.8 28.4 + - - +
305B ILE* 3.7 5.8 - - - +
307B ARG* 1.4 71.4 - - - +
309B ARG* 1.3 62.2 + - - +
311B GLU* 3.4 8.8 + - - +
312B LEU* 3.1 22.1 + - - +
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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
----------------------------------------------------------
842A GLU* 4.5 11.1 + - - -
910A MET* 4.3 16.4 - - - +
247B LEU* 2.8 47.1 + - - +
248B TYR* 3.7 35.4 + - - -
253B LEU* 3.6 23.4 - - + +
256B ARG* 5.8 0.4 - - - +
305B ILE* 3.0 31.9 + - - +
306B GLN* 3.8 4.7 - - - +
307B ARG 3.3 0.2 - - - -
308B LEU* 1.3 74.4 - - - +
310B CYS* 1.3 57.5 + - - +
312B LEU* 3.4 5.7 + - - +
313B ASP* 3.1 27.9 + - - +
435B PRO* 4.2 8.9 + - - +
436B ASP* 2.7 38.5 + - + +
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Residues in contact with CYS 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B GLN 6.1 0.4 - - - -
298B LEU* 3.5 26.9 - - - -
301B ILE* 3.8 15.7 - - + -
306B GLN 3.0 19.3 + - - +
307B ARG 3.5 3.8 - - - +
309B ARG* 1.3 72.7 - - - +
311B GLU* 1.3 59.7 + - - +
313B ASP* 3.5 2.8 + - - +
314B ILE* 3.1 40.6 + - - +
434B SER* 4.3 20.7 - - - -
435B PRO 3.5 17.0 + - - +
436B ASP 4.2 2.5 - - - -
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ILE* 4.1 5.1 - - + +
281B SER* 2.6 34.4 - - - +
284B VAL* 3.4 13.7 - - + +
285B ALA* 3.3 20.5 - - - +
288B LEU* 3.8 22.5 - - + +
298B LEU* 4.3 9.6 - - + +
307B ARG* 3.0 29.1 + - - +
308B LEU* 3.6 14.5 - - - +
309B ARG 3.3 0.2 - - - -
310B CYS* 1.3 73.9 - - - +
312B LEU* 1.3 60.6 + - - +
314B ILE* 3.3 4.7 + - - +
315B MET* 2.9 47.1 + - + +
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Residues in contact with LEU 312 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 3.7 33.2 - - + +
256B ARG* 3.6 55.6 - - + +
257B ILE* 3.5 22.0 - - + -
260B GLN* 5.8 2.5 - - + -
308B LEU 3.1 9.8 + - - +
309B ARG* 3.6 8.7 - - - +
311B GLU* 1.3 74.9 - - - +
313B ASP* 1.3 56.7 + - - +
315B MET* 3.5 11.3 + - + +
316B ASN* 2.9 49.2 + - - +
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Residues in contact with ASP 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
842A GLU* 5.0 6.6 - - - +
309B ARG 3.1 16.3 + - - +
310B CYS 3.8 5.8 - - - +
311B GLU 3.2 0.2 - - - -
312B LEU* 1.3 75.1 - - - +
314B ILE* 1.3 59.4 + - + +
316B ASN* 3.3 6.1 + - - +
317B LYS* 2.9 61.0 + - - +
433B ILE 4.0 0.9 - - - +
434B SER* 4.5 1.2 - - - -
435B PRO* 2.7 45.1 - - - +
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Residues in contact with ILE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B LEU* 4.0 22.7 - - + -
289B PRO* 6.5 0.4 - - + -
290B ILE* 3.6 47.6 - - + -
294B LEU* 4.8 10.8 - - + +
298B LEU* 4.8 4.3 - - + -
310B CYS* 3.1 32.0 + - - +
311B GLU* 3.3 6.5 + - - +
313B ASP* 1.3 75.2 - - + +
315B MET* 1.3 59.6 + - - +
317B LYS* 4.7 1.6 - - - -
318B CYS* 3.0 47.8 + - + +
432B GLU* 5.8 0.9 - - - +
433B ILE 6.0 0.2 - - - +
434B SER* 4.7 16.6 - - - -
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Residues in contact with MET 315 (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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257B ILE* 3.8 29.6 - - + -
260B GLN* 3.5 40.0 + - + +
261B LEU* 5.3 0.7 - - - -
264B TRP* 4.3 16.4 - - + -
284B VAL* 3.8 23.1 - - + -
288B LEU* 3.9 18.2 - - + -
311B GLU* 2.9 35.7 + - + +
312B LEU* 3.6 11.2 - - + +
314B ILE* 1.3 75.3 - - - +
316B ASN* 1.3 60.2 + - - +
318B CYS 4.8 2.0 - - - -
334B LYS* 2.8 31.3 + - - +
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Residues in contact with ASN 316 (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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256B ARG* 4.5 9.9 - - - +
260B GLN* 4.5 7.3 + - - -
312B LEU* 2.9 38.1 + - - +
313B ASP* 4.0 6.7 + - - +
314B ILE 3.2 0.2 - - - -
315B MET* 1.3 83.0 - - - +
317B LYS* 1.4 63.8 + - + +
319B THR* 3.5 16.9 - - - +
334B LYS* 3.9 9.5 + - - +
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Residues in contact with LYS 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313B ASP* 2.9 42.0 + - - +
314B ILE* 4.2 0.9 - - - +
316B ASN* 1.4 77.7 - - + +
318B CYS* 1.3 65.5 + - - +
319B THR* 3.1 8.7 + - - +
426B ILE* 4.0 26.1 - - + +
427B PRO* 3.6 18.9 - - - +
430B GLU* 5.7 5.1 + - - -
432B GLU* 5.1 1.3 - - - +
433B ILE* 2.9 50.2 + - - +
435B PRO* 3.5 13.4 - - - +
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Residues in contact with CYS 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B ILE* 5.8 0.2 - - + -
294B LEU* 5.1 1.3 - - - -
314B ILE* 3.0 41.4 + - + +
315B MET* 4.5 1.6 - - - +
316B ASN 4.8 0.2 - - - -
317B LYS* 1.3 74.1 - - - +
319B THR* 1.3 63.6 + - - +
320B SER 3.6 1.7 - - - +
334B LYS* 4.2 13.0 - - - +
424B PRO* 3.8 31.9 - - + -
425B THR 3.5 11.4 - - - +
426B ILE* 4.4 4.5 - - - -
432B GLU* 3.3 26.5 - - - -
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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