Contacts of the helix formed by residues 294 - 308 (chain A) in PDB entry 2QQ6
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 GLY 294 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A TYR* 3.6 31.4 - - - -
86A ILE* 3.9 6.3 - - - -
90A SER* 2.6 23.8 + - - -
93A GLU* 3.1 16.3 - - - +
293A CYS* 1.3 76.0 - - - +
295A GLY* 1.3 61.6 + - - +
298A GLU* 3.6 10.6 - - - +
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Residues in contact with GLY 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A SER* 3.3 14.9 + - - -
93A GLU* 3.3 9.6 - - - -
94A THR* 4.7 0.2 - - - -
290A VAL* 3.1 23.8 + - - +
293A CYS* 4.6 0.5 - - - -
294A GLY* 1.3 78.4 - - - +
296A LEU* 1.3 69.0 + - - -
297A ALA 3.3 2.7 - - - -
298A GLU* 3.2 2.4 + - - +
299A ALA* 2.9 22.9 + - - +
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 2.9 11.1 + - - +
94A THR* 3.8 23.3 - - + +
97A TRP* 3.9 18.8 - - + +
108A VAL* 3.5 32.1 - - + -
112A LEU* 4.5 11.4 - - + +
290A VAL* 3.6 16.4 - - + -
295A GLY* 1.3 69.8 - - - -
297A ALA* 1.3 56.9 + - - +
299A ALA* 3.2 2.7 + - - +
300A LYS* 2.8 30.7 + - - +
326A ALA* 3.8 25.4 - - + +
330A VAL* 3.5 28.4 - - + +
375A LEU* 4.7 7.4 - - + -
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Residues in contact with ALA 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A VAL* 5.1 2.0 - - + -
65A GLU* 4.3 24.0 - - + +
68A TYR* 5.6 5.6 - - + -
93A GLU* 3.1 16.6 + - + +
97A TRP* 3.7 23.8 - - + +
112A LEU* 5.0 3.8 - - - -
296A LEU* 1.3 80.0 - - - +
298A GLU* 1.3 65.3 + - - +
300A LYS* 3.3 6.0 + - - +
301A ARG* 3.3 22.5 + - - +
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Residues in contact with GLU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68A TYR* 3.7 20.4 + - + +
72A ARG* 5.0 1.2 + - - -
93A GLU* 3.7 1.8 + - - -
269A TYR 4.7 0.2 - - - +
270A THR* 3.8 9.4 - - - +
271A ARG* 3.0 68.6 + - - +
293A CYS* 4.0 16.4 - - - +
294A GLY* 3.6 19.1 - - - +
295A GLY 3.2 8.3 + - - +
297A ALA* 1.3 80.8 - - - +
299A ALA* 1.3 64.7 + - - +
301A ARG* 3.1 16.5 + - - +
302A ILE* 3.1 23.9 + - + +
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Residues in contact with ALA 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A PRO* 5.4 3.4 - - + -
290A VAL* 4.3 18.6 - - + +
293A CYS* 4.6 7.3 - - - -
295A GLY 2.9 13.3 + - - +
296A LEU* 3.4 11.0 - - - +
298A GLU* 1.3 74.8 - - - +
300A LYS* 1.3 66.3 + - - +
302A ILE* 3.3 14.7 + - - +
303A ALA* 3.0 21.8 + - - +
313A PHE* 4.1 10.2 - - + -
330A VAL* 4.0 16.8 - - + -
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Residues in contact with LYS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A LEU* 2.9 44.6 + - + +
113A GLY* 4.5 4.6 - - - -
296A LEU 2.8 18.4 + - - +
297A ALA* 3.8 7.0 - - - +
299A ALA* 1.3 71.7 - - - +
301A ARG* 1.3 65.8 + - + +
303A ALA* 2.9 7.5 + - - +
304A ASN* 2.8 49.3 + - - +
330A VAL* 4.0 12.9 - - + +
333A ALA* 4.3 14.8 - - + +
334A VAL* 4.5 9.6 - - + -
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A GLU* 4.1 23.4 + - - +
69A GLU* 5.8 4.4 - - - +
271A ARG* 3.2 55.0 - - + +
297A ALA 3.3 12.1 + - - +
298A GLU* 3.1 12.6 + - - +
300A LYS* 1.3 79.4 - - + +
302A ILE* 1.3 55.2 + - - +
304A ASN* 2.6 36.2 + - - +
305A LEU* 2.8 18.1 + - + +
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Residues in contact with ILE 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A TYR 4.2 4.5 - - - +
271A ARG* 4.1 15.3 - - - -
274A PHE* 3.3 58.8 - - + -
278A PHE* 3.8 5.9 - - + -
286A VAL* 5.3 2.7 - - + -
288A PRO* 4.1 19.1 - - + -
293A CYS* 4.3 8.1 - - - -
298A GLU* 3.1 31.9 + - + +
299A ALA* 3.3 11.9 + - - +
301A ARG* 1.3 77.9 - - - +
303A ALA* 1.3 63.6 + - - +
305A LEU* 3.2 11.8 + - - +
306A ALA* 3.1 21.3 + - - +
313A PHE* 5.0 1.3 - - + -
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A ALA 3.0 10.4 + - - +
300A LYS 2.9 10.1 + - - +
302A ILE* 1.3 76.2 - - - +
304A ASN* 1.3 58.2 + - - +
306A ALA* 3.3 5.0 + - - +
307A GLU* 2.9 25.1 + - - +
313A PHE* 3.7 30.5 - - + -
334A VAL* 3.3 31.9 - - + -
336A ASN* 3.3 11.7 + - - +
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Residues in contact with ASN 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300A LYS* 2.8 46.8 + - - +
301A ARG* 2.6 23.2 + - - +
303A ALA* 1.3 75.7 - - - +
305A LEU* 1.3 59.7 + - + +
307A GLU* 3.3 21.2 + - - +
308A LEU* 3.6 14.2 + - - +
333A ALA 5.6 0.2 - - - +
334A VAL* 4.5 5.5 - - - +
336A ASN* 5.7 0.3 + - - -
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Residues in contact with LEU 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A ARG* 4.1 17.3 - - + +
274A PHE* 4.6 0.7 - - + -
275A ARG* 4.0 34.3 - - + +
278A PHE* 3.7 16.9 - - + -
301A ARG* 2.8 14.5 + - + +
302A ILE* 3.4 14.4 - - - +
304A ASN* 1.3 78.3 - - + +
306A ALA* 1.3 62.4 + - - +
308A LEU* 3.3 34.4 + - + +
309A ASP* 4.1 6.6 + - - +
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Residues in contact with ALA 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A PHE* 3.2 36.1 - - + -
286A VAL* 3.8 12.3 - - + -
302A ILE 3.1 5.6 + - - +
303A ALA* 3.6 9.2 - - - +
305A LEU* 1.3 79.8 - - - +
307A GLU* 1.3 63.0 + - - +
309A ASP* 3.0 8.5 + - - -
311A ILE* 3.0 40.7 + - + +
312A PRO 5.5 0.2 - - - -
313A PHE* 5.7 0.2 - - + -
336A ASN* 3.9 2.5 - - - +
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Residues in contact with GLU 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303A ALA 2.9 13.3 + - - +
304A ASN* 3.3 16.5 - - - +
306A ALA* 1.3 77.8 - - - +
308A LEU* 1.3 74.7 + - - +
309A ASP 3.0 0.2 - - - -
310A TYR* 3.0 28.8 + - - +
311A ILE 4.6 0.7 - - - +
335A SER* 3.8 22.1 + - - +
336A ASN* 3.3 23.3 + - + +
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A ASN 3.6 15.0 - - - +
305A LEU* 3.3 23.5 + - + +
306A ALA 3.2 0.6 - - - -
307A GLU* 1.3 87.2 - - - +
309A ASP* 1.3 63.9 + - - +
310A TYR* 4.3 13.2 + - - -
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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