Contacts of the helix formed by residues 336 - 354 (chain A) in PDB entry 3Q29
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 336 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A GOL 2.8 26.7 + - - -
170A PHE* 3.5 28.0 - - + -
179A ILE* 3.9 26.1 - - + +
334A ILE* 2.9 9.3 + - + -
335A PRO* 1.3 78.6 - - - +
337A MET* 1.3 65.0 + - - +
338A SER 3.1 0.4 - - - -
339A ALA* 3.1 18.5 + - - +
340A PHE* 3.1 15.2 + - - +
369A SER 2.9 20.1 + - - +
370A SER 3.1 19.8 + - - -
371A SER* 3.5 14.2 + - - +
372A MET 4.7 1.0 - - - +
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Residues in contact with MET 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP* 4.1 16.6 - - + +
67A ARG* 6.0 0.2 - - - -
169A ALA* 4.6 2.9 - - + -
170A PHE* 3.8 22.0 - - - -
259A PHE* 4.9 0.9 - - + -
331A MET* 4.8 2.2 - - + -
332A PRO* 3.4 55.0 - - + +
334A ILE* 2.9 20.0 + - + +
336A GLN* 1.3 78.6 - - - +
338A SER* 1.3 56.7 + - - +
340A PHE* 3.1 24.2 + - + +
341A TRP* 2.9 69.0 + - + +
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Residues in contact with SER 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GOL 3.2 15.9 - - - -
67A ARG* 3.2 35.5 + - - +
335A PRO 3.7 3.4 + - - -
336A GLN 3.1 0.8 - - - -
337A MET* 1.3 78.7 - - - +
339A ALA* 1.3 61.2 + - - +
341A TRP* 3.2 5.7 + - - +
342A TYR* 3.1 38.1 + - - -
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Residues in contact with ALA 339 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A GOL 2.9 29.9 + - - +
336A GLN* 3.1 19.5 + - - +
338A SER* 1.3 72.6 - - - +
340A PHE* 1.3 66.8 + - - +
342A TYR* 3.3 11.3 + - - +
343A ALA* 3.0 24.9 + - - +
368A ASN 4.2 12.8 - - - +
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Residues in contact with PHE 340 (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 TRP* 3.9 19.7 - + - -
169A ALA* 3.6 30.5 - - + -
170A PHE* 4.0 18.6 - + + -
182A VAL* 4.9 0.9 - - + -
184A VAL* 3.5 25.6 - - + -
259A PHE* 4.3 2.2 - + - -
336A GLN 3.1 12.2 + - - +
337A MET* 3.2 35.9 - - + +
339A ALA* 1.3 78.5 - - - +
341A TRP* 1.3 92.7 + + - +
343A ALA* 3.3 1.4 + - - +
344A VAL* 3.0 35.1 + - + +
369A SER* 3.5 27.9 - - - +
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Residues in contact with TRP 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASP* 2.9 25.8 + - - -
67A ARG* 3.7 24.5 - - - +
155A PRO* 3.7 26.3 - - + +
156A TYR* 4.2 8.7 - + - -
159A TRP* 5.4 3.6 - + + -
259A PHE* 3.3 34.5 - + - -
331A MET* 3.7 23.6 - - - -
337A MET* 2.9 40.7 + - + +
338A SER 3.6 7.2 - - - +
340A PHE* 1.3 88.5 - + - +
342A TYR* 1.3 61.2 + - + +
344A VAL* 5.1 1.6 - - + -
345A ARG* 2.9 34.0 + - - +
2B GLC 3.5 39.0 - - - +
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Residues in contact with TYR 342 (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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46A GLU* 3.0 32.5 + - + +
67A ARG* 5.0 8.0 + - - -
338A SER* 3.1 37.2 + - - -
339A ALA* 3.3 9.4 + - - +
341A TRP* 1.3 76.9 - - + +
343A ALA* 1.3 58.5 - - - +
345A ARG* 3.4 43.5 + - - +
346A THR* 2.9 34.7 + - - +
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A ALA 3.0 16.8 + - - +
340A PHE 3.6 0.2 - - - +
342A TYR* 1.3 77.6 - - - +
344A VAL* 1.3 57.3 + - - +
346A THR* 3.5 6.4 + - - -
347A ALA 3.0 20.4 + - - -
365A ALA* 3.6 18.7 - - - +
368A ASN* 3.9 15.5 - - + +
369A SER* 3.5 34.3 - - - +
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Residues in contact with VAL 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A PRO* 3.7 19.1 - - + -
159A TRP* 4.3 21.1 - - + -
162A ILE* 4.8 2.9 - - + -
184A VAL* 4.0 17.9 - - + -
340A PHE* 3.0 45.2 + - + +
341A TRP* 4.3 2.2 - - + +
343A ALA* 1.3 73.3 - - - +
345A ARG* 1.3 67.3 + - - +
346A THR 3.2 0.4 - - - -
347A ALA* 3.8 6.2 - - + +
348A VAL* 3.0 34.2 + - + +
362A LEU* 5.8 3.8 - - + -
365A ALA* 4.4 3.8 - - + -
369A SER* 4.1 4.3 - - - +
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Residues in contact with ARG 345 (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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45A GLU* 5.7 1.4 + - - -
46A GLU* 3.6 12.9 + - - -
153A GLN 3.8 12.8 + - - +
154A GLU* 4.9 12.5 + - - +
155A PRO* 3.7 30.8 - - + +
341A TRP 2.9 20.2 + - - +
342A TYR* 3.4 43.2 + - - +
344A VAL* 1.3 77.7 - - - +
346A THR* 1.3 67.5 + - - +
348A VAL* 4.0 1.3 - - - +
349A ILE* 3.0 42.4 + - + +
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Residues in contact with THR 346 (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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342A TYR 2.9 19.0 + - - -
343A ALA* 3.6 7.2 - - - -
345A ARG* 1.3 83.6 + - - +
347A ALA* 1.3 57.6 + - - +
349A ILE* 3.8 4.3 - - - +
350A ASN* 2.8 53.8 + - - +
356A GLN* 5.0 2.2 - - - +
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Residues in contact with ALA 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193A LEU* 4.8 1.6 - - - -
343A ALA 3.0 8.3 + - - +
344A VAL* 3.3 5.1 + - - +
346A THR* 1.3 77.7 - - - +
348A VAL* 1.3 58.0 + - + +
350A ASN* 4.5 1.6 - - - -
351A ALA* 2.8 33.5 + - - +
356A GLN* 5.0 1.6 - - - -
361A ALA* 3.3 37.6 - - + +
362A LEU* 4.3 11.2 - - + -
365A ALA* 3.6 21.1 - - + -
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Residues in contact with VAL 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A LEU* 4.2 15.5 - - + +
155A PRO* 4.5 11.2 - - + -
158A THR* 3.9 26.0 - - + +
162A ILE* 3.9 27.8 - - + -
193A LEU* 4.6 9.1 - - + +
196A LEU* 4.2 12.6 - - + -
344A VAL* 3.0 30.2 + - + +
345A ARG* 4.0 3.6 - - - +
347A ALA* 1.3 72.1 - - + +
349A ILE* 1.3 58.8 + - + +
351A ALA* 3.9 3.5 - - - +
352A ALA* 2.7 39.9 + - + +
362A LEU* 6.0 0.4 - - + -
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Residues in contact with ILE 349 (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 LEU 4.2 13.5 - - - +
153A GLN* 3.7 42.0 - - + +
207A ALA* 5.7 0.2 - - - +
345A ARG* 3.0 36.1 + - + +
346A THR* 4.0 4.5 - - - +
348A VAL* 1.3 76.0 - - + +
350A ASN* 1.3 67.0 + - - +
352A ALA* 3.8 5.1 - - - +
353A SER* 3.0 33.4 + - - +
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Residues in contact with ASN 350 (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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346A THR* 2.8 36.0 + - - +
347A ALA 3.9 2.2 - - - +
349A ILE* 1.3 83.0 - - - +
351A ALA* 1.3 60.9 + - - +
353A SER* 3.8 4.2 + - - -
354A GLY 3.0 23.2 + - - -
355A ARG* 3.0 42.7 + - - +
356A GLN* 2.9 42.8 + - + +
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Residues in contact with ALA 351 (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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193A LEU* 3.8 24.9 - - + -
197A VAL* 3.6 30.4 - - + +
347A ALA 2.8 20.8 + - - +
348A VAL 3.9 2.0 - - - +
350A ASN* 1.3 73.3 - - - +
352A ALA* 1.3 63.9 + - - +
354A GLY* 3.3 10.2 + - - -
356A GLN 3.4 14.2 + - - +
358A VAL* 4.2 7.6 - - + -
361A ALA* 4.2 9.3 - - + +
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Residues in contact with ALA 352 (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 LEU* 5.6 6.1 - - + +
196A LEU* 5.2 4.0 - - + -
197A VAL* 4.3 7.6 - - - +
200A ILE* 3.7 39.0 - - + +
207A ALA* 3.5 24.3 - - + +
348A VAL* 2.7 29.5 + - + +
349A ILE* 3.8 6.1 - - - +
351A ALA* 1.3 76.4 - - - +
353A SER* 1.3 60.1 + - - +
354A GLY* 4.7 0.2 - - - -
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Residues in contact with SER 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A ALA* 4.0 13.0 - - - -
208A ASP* 6.1 1.1 - - - -
349A ILE* 3.0 21.7 + - - +
350A ASN* 3.2 6.4 + - - -
352A ALA* 1.3 76.7 - - - +
354A GLY* 1.3 60.8 + - - +
355A ARG* 3.2 19.9 + - - +
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Residues in contact with GLY 354 (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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350A ASN 3.0 6.2 + - - -
351A ALA 3.3 6.2 + - - -
352A ALA 3.3 4.4 + - - -
353A SER* 1.3 78.7 - - - +
355A ARG* 1.3 65.5 + - - +
356A GLN* 3.1 9.8 + - - +
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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
------------------------------------------------------------
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