Contacts of the helix formed by residues 326 - 338 (chain A) in PDB entry 2Q8I
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 TYR 326 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A VAL* 5.1 4.9 - - + -
127A ALA* 3.6 25.2 + - + +
130A VAL* 3.2 31.4 - - - +
131A ILE* 4.8 8.7 - - + +
151A LEU* 4.7 1.2 - - + +
155A TYR* 3.2 33.4 - + - -
303A TYR* 3.6 50.3 + + + +
306A SER* 4.2 11.7 - - - -
325A GLY* 1.3 71.0 - - - +
327A GLY* 1.3 62.7 + - - +
328A LEU 3.2 2.0 - - - -
329A PRO* 3.1 11.3 - - - +
330A ILE* 3.0 39.9 + - + +
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Residues in contact with GLY 327 (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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243A HIS* 4.9 2.9 + - - -
247A GLU* 3.4 31.3 - - - +
325A GLY 2.9 12.5 - - - +
326A TYR* 1.3 78.5 - - - +
328A LEU* 1.3 53.6 + - - +
330A ILE* 4.1 3.8 - - - +
331A SER* 2.7 36.0 + - - -
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLU* 5.3 2.5 - - + -
248A LEU* 4.2 10.5 - - + -
251A ASN* 4.6 8.6 - - - +
300A LEU* 3.6 27.1 - - + +
301A PHE* 3.6 28.5 - - + -
325A GLY 4.3 2.7 + - - +
327A GLY* 1.3 76.4 - - - +
329A PRO* 1.3 72.5 - - + +
331A SER* 3.2 3.9 + - - -
332A ARG* 3.0 20.1 + - - +
342A LEU* 4.0 21.1 - - + -
344A LEU* 4.3 5.8 - - + -
408A RDC 3.6 44.6 - - + +
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Residues in contact with PRO 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ASP* 5.0 1.6 - - - +
300A LEU 3.8 13.9 - - - +
301A PHE* 3.5 38.1 - - + +
302A ASN 5.5 0.2 - - - -
303A TYR* 3.7 31.6 - - + +
306A SER* 6.0 1.3 - - - -
325A GLY 4.1 5.2 - - - +
326A TYR* 3.1 22.9 - - - +
328A LEU* 1.3 95.3 - - + +
330A ILE* 1.3 54.4 + - - +
332A ARG* 3.1 8.8 + - + +
333A LEU* 2.9 32.2 + - - +
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Residues in contact with ILE 330 (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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123A VAL* 4.3 20.4 - - + -
155A TYR* 4.3 12.3 - - + -
159A ILE* 4.9 7.0 - - + -
243A HIS* 4.2 11.2 - - + +
303A TYR* 4.3 8.7 - - + -
326A TYR* 3.0 44.6 + - + +
327A GLY* 4.3 3.1 - - - +
329A PRO* 1.3 73.4 - - - +
331A SER* 1.3 64.7 + - - +
333A LEU* 3.0 27.5 + - + +
334A TYR* 3.0 35.6 + - + -
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Residues in contact with SER 331 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A HIS* 3.9 3.3 - - - -
244A MET* 3.5 33.4 - - - +
247A GLU* 3.4 22.9 - - - +
248A LEU* 5.5 1.1 - - - -
327A GLY 2.7 23.5 + - - -
328A LEU* 3.2 7.4 + - - -
330A ILE* 1.3 74.2 - - - +
332A ARG* 1.3 66.0 + - - +
334A TYR* 3.2 5.4 + - - -
335A ALA* 3.1 17.0 + - - +
342A LEU* 3.7 17.7 - - - +
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Residues in contact with ARG 332 (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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148A GLN* 5.3 4.0 - - - +
152A ASP* 4.9 11.3 + - - -
301A PHE* 3.5 59.4 + - + +
328A LEU 3.0 13.1 + - - +
329A PRO* 3.4 11.0 - - - +
331A SER* 1.3 75.4 - - - +
333A LEU* 1.3 69.4 + - - +
335A ALA* 3.1 2.4 + - - +
336A ARG* 2.9 77.2 + - - +
342A LEU* 3.7 35.8 + - + +
409A GOL 4.3 8.7 + - - -
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Residues in contact with LEU 333 (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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152A ASP* 3.8 36.8 - - + +
155A TYR* 3.4 34.1 - - + -
156A THR* 3.6 22.2 + - - +
159A ILE* 4.2 10.4 - - + +
303A TYR* 3.5 14.6 - - - +
329A PRO 2.9 17.3 + - - +
330A ILE* 3.0 16.5 + - + +
332A ARG* 1.3 84.8 - - - +
334A TYR* 1.3 61.1 + - - +
336A ARG* 4.0 8.5 - - + +
337A TYR* 3.1 25.6 + - - +
368A ARG* 6.2 2.5 - - - +
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Residues in contact with TYR 334 (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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159A ILE* 3.8 33.8 - - + +
236A TYR* 3.8 12.1 + - - -
240A HIS* 3.5 48.0 + + + +
243A HIS* 3.9 38.7 + + + -
244A MET* 3.8 17.9 - - + -
330A ILE* 3.0 42.0 + - + -
331A SER* 3.6 7.2 - - - +
332A ARG 3.2 0.4 - - - -
333A LEU* 1.3 75.9 - - - +
335A ALA* 1.3 63.7 + - - +
337A TYR* 3.3 19.3 - - - +
338A PHE 4.1 0.9 + - - -
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Residues in contact with ALA 335 (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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236A TYR* 4.7 4.7 + - - -
244A MET* 3.6 22.6 - - - -
331A SER 3.1 8.1 + - - +
332A ARG 3.1 6.0 + - - +
334A TYR* 1.3 75.2 - - - +
336A ARG* 1.4 57.2 + - - +
337A TYR 2.8 8.6 + - - -
338A PHE 3.6 3.3 + - - -
340A GLY* 2.9 25.5 + - - -
341A ASP 3.3 33.2 - - - +
342A LEU* 4.0 4.9 - - + +
356A ILE* 4.7 4.3 - - + -
357A TYR 4.7 1.1 - - - +
358A LEU* 5.0 2.2 - - - +
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Residues in contact with ARG 336 (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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152A ASP* 5.2 6.3 + - - -
332A ARG* 2.9 71.7 + - + +
333A LEU* 3.3 10.1 + - + +
335A ALA* 1.4 72.0 - - - +
337A TYR* 1.3 63.2 + - - +
338A PHE 3.5 0.2 - - - -
339A GLN* 3.1 12.3 + - - -
340A GLY 3.1 13.0 - - - +
341A ASP* 2.8 45.3 + - - +
342A LEU 5.1 0.2 + - - -
368A ARG* 3.6 48.3 - - - +
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Residues in contact with TYR 337 (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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156A THR* 4.1 15.0 - - + -
159A ILE* 3.8 22.7 - - + -
160A SER* 3.5 25.9 - - - -
163A MET* 3.4 23.4 - - + +
240A HIS* 3.9 14.6 - + - -
333A LEU 3.1 19.2 + - - +
334A TYR* 3.3 10.5 - - - +
335A ALA 2.8 2.0 - - - -
336A ARG 1.3 82.7 - - - +
338A PHE* 1.4 89.6 + + - -
339A GLN 3.3 0.4 - - - -
367A GLU* 2.9 37.0 + - + +
368A ARG* 3.0 39.1 + - - +
369A LEU* 4.3 3.4 - - + -
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Residues in contact with PHE 338 (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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27A LEU 4.3 0.9 - - - -
29A ILE* 3.7 36.8 - - + -
32A PHE* 4.3 9.6 - + - -
163A MET* 4.3 17.0 - - + -
236A TYR* 4.2 25.1 - + + +
237A VAL* 4.2 18.8 - - + -
240A HIS* 4.4 4.0 - + - -
334A TYR 4.1 1.6 + - - -
335A ALA 3.6 4.2 + - - -
336A ARG 3.5 0.2 - - - -
337A TYR* 1.4 112.0 - + - +
339A GLN* 1.3 72.1 + - - +
340A GLY 3.3 2.7 + - - -
359A LYS* 3.9 7.3 + - - +
365A SER* 3.5 31.0 - - - -
366A PHE 3.6 2.7 - - - -
367A GLU* 3.8 28.9 - - + -
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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