Contacts of the helix formed by residues 299 - 312 (chain A) in PDB entry 2QMQ
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 299 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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288A MET* 3.3 21.7 - - + +
290A ASP* 3.1 30.1 + - - +
291A SER* 3.8 15.5 - - - +
295A PRO 2.9 13.4 + - - +
298A THR* 1.3 93.9 + - - +
300A PRO* 1.3 63.7 - - - +
301A GLY 3.2 3.5 + - - +
302A LYS* 3.3 31.3 + - + +
303A LEU* 3.0 21.1 + - - +
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Residues in contact with PRO 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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81A PRO* 4.3 10.5 - - + +
82A LEU* 3.9 24.4 - - + +
85A PHE* 3.8 33.9 - - + -
295A PRO 4.1 0.8 - - - +
296A GLN 4.4 5.6 - - - +
297A LEU 4.1 11.4 - - - +
298A THR 3.2 9.9 - - - +
299A GLN* 1.3 90.5 - - - +
301A GLY* 1.3 55.4 + - - +
303A LEU* 3.7 1.5 - - + -
304A THR* 2.7 39.1 + - - -
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Residues in contact with GLY 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A PHE* 3.5 24.8 - - - -
299A GLN 3.2 1.2 - - - -
300A PRO* 1.3 85.3 - - - +
302A LYS* 1.3 62.2 + - - +
304A THR* 3.3 8.8 + - - -
305A GLU* 3.3 13.0 + - - +
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Residues in contact with LYS 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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286A LEU* 4.6 4.8 - - + +
288A MET* 3.7 27.0 - - + +
289A ALA* 5.3 11.1 - - - +
290A ASP* 4.8 12.5 + - - +
299A GLN* 3.3 32.5 + - - +
301A GLY* 1.3 74.0 - - - +
303A LEU* 1.3 63.4 + - - +
305A GLU* 3.4 7.7 + - - +
306A ALA* 3.3 19.2 + - - +
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Residues in contact with LEU 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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82A LEU* 3.9 17.7 - - + -
167A VAL* 5.2 0.4 - - + -
169A ILE* 4.4 8.3 - - + -
258A MET* 4.3 7.0 - - + -
260A VAL* 3.9 33.0 - - + -
286A LEU* 4.5 5.6 - - + -
288A MET* 4.7 4.0 - - + +
295A PRO* 4.5 5.2 - - + +
296A GLN* 3.7 39.5 - - + +
299A GLN 3.0 16.1 + - - +
300A PRO 4.0 2.9 - - - +
302A LYS* 1.3 74.2 - - - +
304A THR* 1.3 60.6 + - - +
306A ALA* 3.2 7.7 + - + +
307A PHE* 2.8 58.9 + - + -
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Residues in contact with THR 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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82A LEU* 3.9 4.6 - - - +
85A PHE* 3.5 11.0 - - - -
87A ASP* 3.4 33.4 - - + +
88A MET* 3.4 32.5 - - + +
91A ILE* 3.8 11.4 - - + +
300A PRO 2.7 24.4 + - - -
301A GLY* 3.6 5.6 - - - -
302A LYS 3.3 0.2 - - - -
303A LEU* 1.3 76.5 - - - +
305A GLU* 1.3 57.5 + - - +
307A PHE* 3.1 6.8 + - - +
308A LYS* 2.8 27.8 + - + +
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Residues in contact with GLU 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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301A GLY 3.3 9.2 + - - +
302A LYS* 3.8 8.7 - - - +
303A LEU 3.3 0.4 - - - -
304A THR* 1.3 79.4 - - - +
306A ALA* 1.3 61.4 + - - +
308A LYS* 3.2 7.4 + - + +
309A TYR* 3.1 50.1 + - + -
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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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258A MET* 3.6 30.2 - - + +
286A LEU* 3.6 28.7 - - + -
302A LYS 3.3 5.7 + - - +
303A LEU* 3.3 10.1 - - + +
305A GLU* 1.3 75.3 - - - +
307A PHE* 1.3 58.8 + - - +
309A TYR* 3.2 6.2 + - - +
310A PHE* 2.9 28.2 + - - +
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Residues in contact with PHE 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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65A ILE* 5.8 3.4 - - + -
82A LEU* 3.9 14.4 - - + -
83A PHE* 4.9 3.6 - + - -
88A MET* 3.5 31.6 - - + -
91A ILE* 4.4 4.0 - - + -
92A ILE* 5.3 1.3 - - + -
141A ILE* 6.3 0.4 - - + -
143A VAL* 3.8 42.4 - - + -
167A VAL* 3.8 23.8 - - + -
169A ILE* 5.5 0.7 - - + -
258A MET* 4.2 2.9 - - + -
303A LEU* 2.8 58.2 + - + +
304A THR 3.4 7.4 - - - +
306A ALA* 1.3 69.0 - - - +
308A LYS* 1.3 68.0 + - - +
310A PHE* 3.1 7.2 + + + +
311A LEU* 3.0 43.9 + - + +
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Residues in contact with LYS 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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91A ILE* 4.0 37.6 - - + +
304A THR* 2.8 17.6 + - + +
305A GLU* 3.5 13.0 - - + +
306A ALA 3.2 0.2 - - - -
307A PHE* 1.3 73.9 - - - +
309A TYR* 1.3 93.6 + - + +
311A LEU* 3.7 2.0 - - - +
312A GLN* 2.8 47.4 + - + +
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Residues in contact with TYR 309 (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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305A GLU* 3.1 42.7 + - + +
306A ALA* 3.2 4.5 + - - +
308A LYS* 1.3 105.2 + - + +
310A PHE* 1.3 63.8 + - - +
312A GLN* 3.5 42.2 + - - +
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Residues in contact with PHE 310 (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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141A ILE* 3.9 28.6 - - + +
164A GLU 5.6 0.2 - - - -
165A GLY* 4.0 5.8 - - - -
166A LEU 3.6 20.0 - - - -
167A VAL* 3.9 20.0 - - + -
256A PRO* 3.6 30.5 - - + -
257A VAL 3.9 6.3 - - - -
258A MET* 3.8 35.2 - - + -
284A SER* 4.9 4.3 - - - -
306A ALA 2.9 16.7 + - - +
307A PHE* 3.1 10.3 + + - +
309A TYR* 1.3 79.3 - - - +
311A LEU* 1.3 66.5 + - + +
312A GLN 4.5 2.8 - - - +
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Residues in contact with LEU 311 (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 ILE* 4.4 16.8 - - + -
91A ILE* 3.9 22.2 - - + -
92A ILE* 4.4 3.8 - - + -
95A PHE* 4.0 36.4 - - + -
141A ILE* 3.3 42.6 - - + -
307A PHE* 3.0 30.7 + - + +
308A LYS* 4.0 2.2 - - - +
310A PHE* 1.3 82.2 - - + +
312A GLN* 1.3 69.2 - - - +
313A GLY* 3.5 2.3 + - - -
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Residues in contact with GLN 312 (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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308A LYS* 2.8 41.3 + - + +
309A TYR* 3.5 35.1 + - - +
310A PHE 3.6 4.1 - - - +
311A LEU* 1.3 80.6 - - - +
313A GLY* 1.3 74.7 + - - +
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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
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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