Contacts of the helix formed by residues 296 - 308 (chain C) in PDB entry 2QMR
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 HIS 296 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255C HIS* 3.2 24.8 + - - -
258C VAL* 3.6 31.3 - - + +
259C GLU* 3.8 28.5 - - + -
262C LEU* 4.2 14.3 - - + +
292C VAL 3.8 19.7 - - - -
293C LEU* 2.7 30.8 + - + +
294C VAL 3.4 1.0 + - - -
295C ARG* 1.3 85.5 + - + +
297C LEU* 1.3 66.2 + - - +
298C PRO* 3.2 4.0 - - - +
299C LYS* 2.8 30.5 + - - +
300C LEU* 2.9 12.3 + - + +
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Residues in contact with LEU 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293C LEU* 3.2 19.3 + - + +
294C VAL* 5.0 5.8 - - - +
296C HIS* 1.3 75.0 - - - +
298C PRO* 1.4 68.6 - - + +
299C LYS 2.9 1.4 + - - -
300C LEU* 2.9 23.2 + - + -
301C ILE* 3.0 40.4 + - + +
386C LEU* 5.1 2.7 - - + -
390C TYR* 3.5 55.4 - - + +
393C GLU* 5.2 2.2 - - - +
394C LEU* 4.8 3.6 - - + -
397C HIS* 4.0 32.8 - - + +
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Residues in contact with PRO 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294C VAL 4.9 4.7 - - - +
295C ARG 4.6 3.1 - - - -
296C HIS* 3.3 9.9 - - - +
297C LEU* 1.4 92.5 - - + +
299C LYS* 1.3 62.8 + - + +
302C PRO* 3.1 21.4 - - + +
397C HIS* 3.9 26.7 - - + +
403D LYS* 4.6 2.5 - - + +
404D GLU* 3.2 59.4 - - + +
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Residues in contact with LYS 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259C GLU* 6.0 3.2 - - + +
262C LEU* 3.8 28.4 - - + +
295C ARG 4.2 16.7 + - - -
296C HIS* 2.8 22.0 + - - +
298C PRO* 1.3 81.5 - - + +
300C LEU* 1.3 62.8 + - - +
302C PRO* 3.5 7.2 - - - +
303C VAL* 3.2 27.3 - - + +
404D GLU 5.8 1.6 - - - -
407D PHE* 3.6 26.5 + - - +
408D HIS* 5.3 9.9 - - - +
409D HIS* 5.4 9.9 - - + +
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Residues in contact with LEU 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C LEU* 3.8 13.2 - - + +
280C TRP* 3.5 56.3 - - + +
293C LEU* 3.9 23.1 - - + -
296C HIS* 2.9 15.7 + - + +
297C LEU* 2.9 13.3 + - + +
299C LYS* 1.3 75.6 - - - +
301C ILE* 1.3 61.2 + - + +
303C VAL* 2.9 23.5 + - + +
304C LEU* 2.9 24.8 + - + +
386C LEU* 3.9 24.0 - - + -
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Residues in contact with ILE 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C LEU* 3.0 50.6 + - + +
300C LEU* 1.3 78.8 - - + +
302C PRO* 1.3 64.0 - - + +
303C VAL 3.3 0.2 + - - -
304C LEU* 3.4 5.7 + - - +
305C VAL* 2.8 37.2 + - + +
383C LEU* 4.1 8.1 - - + -
386C LEU* 4.7 8.5 - - + -
394C LEU* 3.7 26.0 - - + -
397C HIS* 3.6 26.5 - - + +
398C ILE* 3.7 28.0 - - + -
401C LEU* 5.1 2.5 - - + -
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Residues in contact with PRO 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297C LEU 3.8 1.1 - - - +
298C PRO* 3.1 28.5 - - + +
299C LYS* 3.5 11.0 - - - +
300C LEU 3.6 0.7 - - - -
301C ILE* 1.3 97.2 - - + +
303C VAL* 1.3 55.2 + - + +
305C VAL* 3.3 1.9 + - - +
306C ASN* 2.9 30.8 + - - +
397C HIS 5.0 3.8 - - - +
401C LEU* 4.1 22.3 - - + +
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Residues in contact with VAL 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262C LEU* 4.5 11.0 - - + +
265C THR* 3.8 33.3 - - + +
266C GLN* 3.5 44.6 - - + +
299C LYS 3.2 17.3 - - - +
300C LEU* 2.9 18.8 + - + +
302C PRO* 1.3 71.3 - - + +
304C LEU* 1.3 66.3 + - - +
306C ASN* 3.4 7.2 + - - +
307C GLY* 3.1 18.5 + - - -
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Residues in contact with LEU 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265C THR* 5.1 3.4 - - + -
277C CYS* 4.2 5.4 - - - -
280C TRP* 4.0 21.1 - - + +
300C LEU* 2.9 25.2 + - + +
301C ILE* 3.6 9.4 - - - +
303C VAL* 1.3 77.6 - - - +
305C VAL* 1.3 57.9 + - - +
307C GLY* 2.9 17.7 + - - -
308C MET* 3.2 26.7 + - + +
379C SER* 3.4 27.6 - - - +
382C ALA* 3.9 17.7 - - + -
383C LEU* 4.1 16.4 - - + +
386C LEU* 3.6 31.2 - - + -
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Residues in contact with VAL 305 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301C ILE* 2.8 36.3 + - + +
302C PRO 3.7 3.1 - - - +
304C LEU* 1.3 72.5 - - - +
306C ASN* 1.3 64.2 + - - +
308C MET* 3.3 21.8 + - - +
309C LYS* 3.9 3.8 + - - +
383C LEU* 4.3 11.2 - - + -
398C ILE* 4.5 3.6 - - + -
401C LEU* 3.8 20.9 - - + -
405C LEU* 3.7 31.0 - - + -
416C SER* 4.7 6.0 + - - +
420C VAL* 4.0 28.5 - - + -
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Residues in contact with ASN 306 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266C GLN* 6.3 1.0 - - - +
302C PRO 2.9 17.3 + - - +
303C VAL* 3.9 6.7 + - - +
305C VAL* 1.3 78.9 - - - +
307C GLY* 1.3 62.1 + - - +
308C MET 3.3 0.3 + - - -
309C LYS* 3.4 40.8 + - - +
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Residues in contact with GLY 307 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303C VAL 3.1 10.2 + - - -
304C LEU 2.9 10.4 + - - -
306C ASN* 1.3 78.3 - - - +
308C MET* 1.3 60.5 + - - +
309C LYS 3.3 7.4 - - - +
375C LEU* 4.1 18.2 - - - +
376C ARG* 3.4 19.4 + - - -
379C SER* 3.8 14.8 - - - -
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Residues in contact with MET 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C LEU* 3.2 23.1 - - + +
305C VAL* 3.5 10.5 - - - +
306C ASN 3.1 1.0 - - - -
307C GLY* 1.3 75.2 - - - +
309C LYS* 1.3 66.4 + - - +
376C ARG* 3.0 30.5 + - - +
379C SER* 3.3 24.5 - - - +
380C ALA* 3.8 16.6 - - - +
383C LEU* 3.1 50.5 - - + -
416C SER* 4.1 10.5 - - - -
419C LEU* 3.9 20.4 - - + +
420C VAL* 4.0 18.8 - - + -
423C ALA* 5.2 1.6 - - - -
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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