Contacts of the helix formed by residues 243 - 264 (chain n) in PDB entry 5M32
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 GLN 243 (chain n).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311j SER 5.7 6.3 - - - +
241n SER* 3.3 3.4 - - - +
242n LEU* 1.3 91.8 - - - +
244n GLU* 1.3 61.5 + - + +
247n LYS* 3.0 20.9 + - - +
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Residues in contact with GLU 244 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424k LEU* 6.4 0.2 - - - -
241n SER 4.4 1.0 + - - -
243n GLN* 1.3 75.5 - - + +
245n PHE* 1.3 67.8 + - - +
247n LYS* 3.2 6.4 + - - +
248n ALA* 2.9 23.4 + - - +
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Residues in contact with PHE 245 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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424k LEU* 5.7 8.7 - - + -
239n ASP* 6.3 3.1 - - + -
241n SER 3.7 15.1 + - - +
243n GLN 3.7 0.4 - - - -
244n GLU* 1.3 77.3 - - - +
246n VAL* 1.3 64.8 + - - +
248n ALA* 3.2 8.6 + - - +
249n PHE* 2.9 25.3 + - - +
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Residues in contact with VAL 246 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242n LEU* 2.3 62.0 + - + +
245n PHE* 1.3 77.8 - - - +
247n LYS* 1.3 61.0 + - - +
249n PHE* 3.2 7.5 + - - +
250n TYR* 2.9 23.7 + - - +
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Residues in contact with LYS 247 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320j THR 5.1 0.2 + - - -
242n LEU 3.1 0.2 + - - -
243n GLN 3.0 20.4 + - - +
244n GLU* 3.6 5.4 - - - +
246n VAL* 1.3 74.9 - - - +
248n ALA* 1.3 64.9 + - - +
250n TYR* 3.2 8.6 + - - +
251n LEU* 2.9 23.7 + - - +
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Residues in contact with ALA 248 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420k ASP* 4.9 16.9 - - + +
421k PRO 4.9 12.3 - - - +
422k ASN* 5.4 4.5 - - + +
424k LEU* 5.5 4.5 - - + -
425k LEU* 5.1 17.9 - - + +
244n GLU 2.9 13.2 + - - +
245n PHE* 3.2 11.0 + - - +
247n LYS* 1.3 77.3 - - - +
249n PHE* 1.3 60.8 + - - +
251n LEU* 3.2 8.4 + - - +
252n LYS* 3.1 24.5 + - - +
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Residues in contact with PHE 249 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425k LEU* 5.7 5.1 - - - +
245n PHE 2.9 16.1 + - - +
246n VAL* 3.6 6.5 - - - +
248n ALA* 1.3 73.5 - - - +
250n TYR* 1.3 67.9 + - - +
252n LYS* 3.7 4.8 + - - +
253n THR* 3.3 21.3 + - - -
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Residues in contact with TYR 250 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320j THR* 0.7 93.5 - - - +
321j ARG* 1.5 66.0 + - + +
246n VAL 2.9 12.6 + - - +
247n LYS* 3.3 12.8 - - - +
249n PHE* 1.3 79.9 - - - +
251n LEU* 1.3 48.7 - - - +
253n THR* 3.4 3.6 + - - -
254n ASN 3.1 11.8 + - - -
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Residues in contact with LEU 251 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320j THR* 0.9 94.7 - - - +
247n LYS 2.9 12.8 + - - +
248n ALA* 3.2 11.0 + - - +
250n TYR* 1.3 66.5 - - - +
252n LYS* 1.3 64.2 + - - +
254n ASN* 3.0 0.7 + - - +
255n ASP* 2.9 20.4 + - - +
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Residues in contact with LYS 252 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422k ASN* 5.3 12.3 - - + -
248n ALA 3.1 12.8 + - - +
249n PHE* 4.2 5.2 - - - +
251n LEU* 1.3 76.8 - - - +
253n THR* 1.3 64.7 + - - +
255n ASP* 3.2 8.0 + - - +
256n GLN* 2.9 25.6 + - - +
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Residues in contact with THR 253 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321j ARG* 5.2 4.0 - - - -
325j LEU* 6.1 4.0 - - - -
249n PHE 3.3 11.9 + - - -
250n TYR* 3.5 10.5 - - - -
251n LEU 3.2 0.4 - - - -
252n LYS* 1.3 77.0 - - - +
254n ASN* 1.3 64.3 + - - +
256n GLN* 3.2 4.1 + - - +
257n MET* 2.8 26.5 + - - +
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Residues in contact with ASN 254 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319j SER 3.1 28.5 - - - +
320j THR* 3.1 16.4 - - - -
321j ARG 4.0 6.9 + - - +
324j GLN* 4.0 17.0 - - + -
325j LEU* 5.2 4.9 - - - +
328j HIS* 5.0 1.6 - - - +
250n TYR 3.1 2.2 + - - -
251n LEU 3.0 1.6 + - - +
253n THR* 1.3 79.2 - - - +
255n ASP* 1.3 63.5 + - - +
257n MET* 3.2 6.8 + - - +
258n VAL* 2.9 24.0 + - - +
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Residues in contact with ASP 255 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396l THR* 5.6 11.7 - - - -
251n LEU 2.9 12.2 + - - +
252n LYS* 3.6 10.3 - - - +
254n ASN* 1.3 76.6 - - - +
256n GLN* 1.3 61.0 + - - +
258n VAL* 3.3 8.8 + - - +
259n VAL* 3.1 20.1 + - - +
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Residues in contact with GLN 256 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252n LYS 2.9 16.5 + - - +
253n THR* 4.0 4.3 - - - +
255n ASP* 1.3 74.0 - - - +
257n MET* 1.3 64.9 + - - +
259n VAL* 3.2 9.9 + - - +
260n VAL* 3.1 21.3 + - - +
295q ASN* 3.9 28.5 - - + +
299q CYS* 5.4 6.1 - - + -
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Residues in contact with MET 257 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325j LEU* 5.4 3.8 - - + -
328j HIS* 3.4 27.8 - - + +
253n THR 2.8 17.8 + - - +
254n ASN* 3.3 8.7 - - - +
256n GLN* 1.3 75.3 - - - +
258n VAL* 1.3 64.9 + - - +
260n VAL* 3.0 10.9 + - - +
261n TYR* 2.9 19.4 + - - +
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Residues in contact with VAL 258 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328j HIS* 4.4 4.9 - - + +
400l ALA* 6.0 5.2 - - + -
254n ASN 2.9 12.3 + - - +
255n ASP* 3.4 12.3 - - - +
257n MET* 1.3 76.1 - - - +
259n VAL* 1.3 65.1 + - - +
261n TYR* 2.8 20.2 + - - +
262n LEU* 2.8 13.9 + - - +
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Residues in contact with VAL 259 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400l ALA* 5.8 3.8 - - - -
255n ASP 3.1 9.8 + - - +
256n GLN* 3.2 13.2 + - - +
258n VAL* 1.3 78.8 - - - +
260n VAL* 1.3 64.8 + - - +
262n LEU* 3.0 9.3 + - - +
263n ALA* 2.9 22.1 + - - +
241q ASN* 5.0 16.2 - - + -
291q LEU* 6.4 1.8 - - + -
295q ASN* 5.1 10.8 - - + -
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Residues in contact with VAL 260 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332j SER* 6.0 5.6 - - - -
256n GLN 3.1 8.3 + - - +
257n MET* 3.0 11.7 + - - +
259n VAL* 1.3 79.0 - - - +
261n TYR* 1.3 55.9 + - - +
263n ALA* 3.2 5.6 + - - -
264n SER* 2.7 40.0 + - - -
292q MET* 6.1 7.6 - - + -
295q ASN* 5.8 6.7 - - + +
296q ILE* 6.1 5.4 - - + -
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Residues in contact with TYR 261 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328j HIS* 4.0 15.9 - - - +
331j ILE* 3.9 29.7 - - + +
332j SER* 4.9 5.8 - - - +
257n MET 2.9 11.2 + - - +
258n VAL* 2.8 18.8 + - - +
260n VAL* 1.3 74.2 - - - +
262n LEU* 1.3 63.0 + - - +
264n SER* 3.8 5.3 + - - -
265n LEU* 3.5 17.3 + - - +
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Residues in contact with LEU 262 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400l ALA* 4.2 28.7 - - + +
404l ILE* 6.0 6.5 - - + +
258n VAL 2.8 10.9 + - - +
259n VAL* 3.2 11.2 - - - +
261n TYR* 1.3 76.0 - - - +
263n ALA* 1.3 65.1 + - - +
265n LEU* 3.0 17.3 - - - +
266n ILE* 3.7 5.4 + - - +
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Residues in contact with ALA 263 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259n VAL 2.9 11.9 + - - +
260n VAL* 3.6 8.5 - - - +
262n LEU* 1.3 71.6 - - - +
264n SER* 1.3 52.0 - - - +
265n LEU 1.8 28.7 + - - -
266n ILE* 2.5 20.0 + - - +
267n ARG* 3.5 7.0 + - - -
288q VAL* 5.0 23.3 - - + +
291q LEU* 5.9 5.6 - - + -
292q MET* 5.7 6.5 - - + -
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Residues in contact with SER 264 (chain n).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331j ILE 4.9 1.9 - - - +
332j SER* 4.6 15.9 - - - -
335j LEU* 2.8 40.8 - - - +
260n VAL* 2.7 22.4 + - - -
261n TYR* 4.0 4.0 - - - -
263n ALA* 1.3 69.3 - - - +
265n LEU* 1.3 56.5 + - - +
267n ARG* 5.2 5.2 - - - +
268n SER* 3.7 10.0 + - - -
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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