Contacts of the helix formed by residues 297 - 317 (chain A) in PDB entry 3QEL
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 ASN 297 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A THR* 5.0 0.2 - - - -
294A ASN* 2.9 29.7 + - - +
295A GLY 3.6 0.2 - - - -
296A LYS* 1.3 76.0 - - - +
298A GLU* 1.3 60.9 + - - +
299A SER* 3.0 15.0 + - - -
300A ALA* 2.9 39.2 + - + +
301A HIS* 3.1 18.7 + - - -
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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
----------------------------------------------------------
33A LEU* 3.4 12.6 - - - +
34A SER* 2.8 42.0 + - - -
38A HIS* 3.5 31.9 + - + +
93A SER* 2.9 33.7 + - - -
94A HIS 4.6 1.7 - - - +
121A LEU* 4.7 2.2 - - + -
122A THR* 4.7 12.7 - - + +
296A LYS 3.1 9.7 + - - +
297A ASN* 1.3 70.5 + - - +
299A SER* 1.3 64.8 + - - +
301A HIS* 3.3 3.5 + - - +
302A ILE* 2.9 35.2 + - + +
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Residues in contact with SER 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A HIS* 3.9 12.1 + - - -
41A ILE* 3.6 35.4 - - - +
297A ASN* 3.0 10.1 + - - -
298A GLU* 1.3 79.2 - - - +
300A ALA* 1.3 62.9 + - - +
302A ILE* 3.4 2.5 + - - +
303A SER* 3.2 22.2 + - - -
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294A ASN* 4.6 3.8 - - - -
297A ASN* 2.9 35.1 + - + +
299A SER* 1.3 75.7 - - - +
301A HIS* 1.3 57.8 + - - +
303A SER* 3.3 7.9 + - - -
304A ASP* 3.1 30.7 + - - +
355A VAL* 3.6 28.1 - - + +
356A THR* 3.9 13.9 - - + -
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Residues in contact with HIS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LEU* 3.6 29.7 + - + +
122A THR* 4.5 4.5 - - + -
140A THR* 3.0 33.9 + - - +
141A VAL* 3.2 29.2 - - + +
292A LEU* 6.4 0.2 - - + -
293A ILE 5.2 1.0 + - - -
294A ASN 3.1 30.4 + - - -
295A GLY* 4.2 0.2 - - - -
297A ASN 3.1 22.0 + - - +
298A GLU* 4.0 4.5 - - - +
300A ALA* 1.3 73.0 - - - +
302A ILE* 1.3 61.4 + - - +
304A ASP* 4.1 3.7 - - - +
305A ALA* 2.9 32.7 + - - +
356A THR* 3.7 27.8 + - + +
367A ARG* 5.1 0.2 - - - -
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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
----------------------------------------------------------
33A LEU* 3.9 19.1 - - + -
38A HIS* 3.6 41.7 - - + +
41A ILE* 4.2 10.5 - - + +
42A PHE* 3.6 39.0 - - + +
45A ALA* 4.6 1.3 - - + -
91A LEU* 4.5 1.3 - - + -
121A LEU* 3.5 21.5 - - + -
298A GLU* 2.9 24.1 + - + +
299A SER 3.8 4.0 - - - +
301A HIS* 1.3 76.2 - - - +
303A SER* 1.3 65.8 + - - +
305A ALA* 4.0 2.1 - - - +
306A VAL* 3.1 27.5 + - + +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A ILE* 5.3 3.3 - - - +
45A ALA* 4.5 12.8 - - - +
52A ARG* 5.8 0.2 + - - -
299A SER 3.2 11.1 + - - -
300A ALA* 3.4 11.9 - - - -
302A ILE* 1.3 82.4 - - - +
304A ASP* 1.3 67.3 + - - +
306A VAL* 4.0 2.6 - - - +
307A ALA* 3.3 19.9 + - - +
355A VAL* 4.2 13.7 - - - +
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Residues in contact with ASP 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A THR* 5.3 3.4 - - + -
300A ALA 3.1 16.3 + - - +
301A HIS* 4.1 5.4 - - - +
303A SER* 1.3 80.2 + - - +
305A ALA* 1.3 64.0 + - - +
307A ALA* 3.2 6.6 + - - +
308A VAL* 3.0 26.5 + - - +
351A TYR* 5.0 4.7 - - - -
354A GLY* 3.5 6.9 - - - -
355A VAL* 3.0 24.4 + - - +
356A THR* 2.7 42.7 + - - +
359A ILE* 3.4 23.0 - - + +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91A LEU* 4.0 14.8 - - + -
119A ILE* 4.2 13.7 - - + -
121A LEU* 3.4 23.3 - - + -
140A THR* 4.3 11.8 - - + +
301A HIS 2.9 19.2 + - - +
302A ILE 4.0 1.6 - - - +
304A ASP* 1.3 76.2 - - - +
306A VAL* 1.3 58.1 + - - +
308A VAL* 3.4 4.5 + - - +
309A VAL* 3.0 35.9 + - - +
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Residues in contact with VAL 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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29A ILE* 5.4 5.2 - - + -
42A PHE* 3.7 33.0 - - + -
45A ALA* 3.7 41.7 - - + +
46A VAL* 3.9 13.5 - - + +
49A ALA* 4.5 7.9 - - + -
52A ARG* 5.4 0.9 - - - +
60A LEU* 5.5 0.2 - - + -
91A LEU* 3.7 9.6 - - + -
302A ILE* 3.1 20.9 + - + +
303A SER 4.0 1.3 - - - +
305A ALA* 1.3 74.0 - - - +
307A ALA* 1.3 61.5 + - - +
309A VAL* 3.9 4.6 - - - +
310A ALA* 2.8 29.7 + - + +
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Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ARG* 4.0 22.0 + - - +
53A HIS* 5.0 0.5 + - - -
303A SER 3.3 11.8 + - - +
304A ASP* 3.2 10.9 + - - +
306A VAL* 1.3 81.5 - - - +
308A VAL* 1.3 62.0 + - - +
310A ALA* 3.9 2.4 - - - +
311A GLN* 3.2 23.2 + - - +
351A TYR* 3.6 39.3 - - + +
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Residues in contact with VAL 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 6.4 0.9 - - + -
140A THR* 5.7 1.1 - - + -
304A ASP 3.0 19.4 + - - +
305A ALA* 3.9 6.1 - - - +
307A ALA* 1.3 75.3 - - - +
309A VAL* 1.3 59.4 + - + +
311A GLN* 3.4 8.0 + - - +
312A ALA* 3.0 25.5 + - - +
346A LEU* 4.5 9.6 - - + -
349A SER* 3.9 26.0 + - - +
351A TYR* 3.7 22.9 - - + +
359A ILE* 3.6 30.7 - - + -
361A PHE* 4.0 19.5 - - + -
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Residues in contact with VAL 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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29A ILE* 3.7 32.8 - - + -
89A ALA* 4.6 11.0 - - + -
91A LEU* 4.3 8.7 - - + -
119A ILE* 4.2 31.2 - - + -
305A ALA* 3.0 26.5 + - - +
306A VAL* 3.9 4.7 - - - +
308A VAL* 1.3 74.7 - - + +
310A ALA* 1.3 63.4 + - - +
312A ALA* 3.3 6.8 + - - +
313A ILE* 2.9 38.7 + - + +
342A PHE* 4.6 2.7 - - + -
346A LEU* 4.3 7.4 - - + -
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Residues in contact with ALA 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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29A ILE* 5.0 0.2 - - - +
49A ALA* 3.7 18.2 - - + -
53A HIS* 3.9 13.2 - - + +
60A LEU* 3.6 30.7 - - + +
306A VAL 2.8 19.6 + - - +
307A ALA* 3.9 3.6 - - - +
309A VAL* 1.3 76.0 - - - +
311A GLN* 1.3 63.6 + - - +
313A ILE* 3.3 3.4 + - - +
314A HIS* 3.0 31.4 + - - +
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Residues in contact with GLN 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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53A HIS* 4.1 19.4 + - + -
307A ALA 3.2 11.3 + - - +
308A VAL* 3.4 10.5 - - - +
310A ALA* 1.3 79.7 - - - +
312A ALA* 1.3 56.7 + - - +
314A HIS* 3.4 3.0 + - - +
315A GLU* 3.0 38.8 + - - +
349A SER* 4.8 8.9 + - - +
350A LYS 3.7 27.1 + - - +
351A TYR* 3.2 32.1 - - + -
352A PRO* 5.5 0.7 - - - +
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Residues in contact with ALA 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 VAL 3.0 13.0 + - - +
309A VAL 3.6 3.1 - - - +
310A ALA 3.2 0.2 - - - -
311A GLN* 1.3 72.3 - - - +
313A ILE* 1.3 62.1 + - - +
315A GLU* 3.4 4.3 + - - +
316A LEU* 2.8 30.3 + - - +
342A PHE* 3.9 8.7 - - + -
345A VAL* 3.7 17.6 - - + +
346A LEU* 3.4 33.2 - - + -
349A SER* 3.9 12.3 - - - +
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Residues in contact with ILE 313 (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 VAL* 4.0 9.0 - - + -
29A ILE* 4.8 1.8 - - + -
58A ILE* 3.2 25.8 - - + -
60A LEU* 4.0 23.6 - - + -
88A TYR* 3.9 24.0 - - + -
309A VAL* 2.9 35.9 + - + +
310A ALA 3.6 4.9 - - - +
312A ALA* 1.3 76.3 - - - +
314A HIS* 1.3 61.4 + - - +
316A LEU* 3.1 12.8 + - + +
317A PHE* 3.1 27.5 + - + -
342A PHE* 3.2 30.5 - - + -
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Residues in contact with HIS 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A ALA 5.3 0.7 - - - -
50A ASN* 5.5 0.4 - - - -
53A HIS* 3.5 42.3 + + + +
54A PHE 3.7 18.7 + - - -
55A THR* 4.1 4.4 - - + +
58A ILE* 3.5 45.3 + - + +
60A LEU* 4.9 14.8 - - + -
310A ALA* 3.0 28.2 + - + +
311A GLN 3.9 3.4 - - - +
313A ILE* 1.3 74.0 - - - +
315A GLU* 1.3 65.0 + - - +
317A PHE* 3.3 12.5 + - - +
318A GLU* 3.4 11.1 + - - +
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Residues in contact with GLU 315 (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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311A GLN* 3.0 29.4 + - - +
312A ALA* 3.7 5.0 - - - +
314A HIS* 1.3 76.6 - - - +
316A LEU* 1.3 62.5 + - - +
318A GLU* 3.2 20.6 + - + +
319A MET* 3.9 19.6 - - + +
345A VAL* 3.8 27.8 - - + +
348A SER* 5.1 4.0 + - - -
349A SER* 5.3 5.1 + - - -
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Residues in contact with LEU 316 (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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88A TYR* 4.4 17.7 - - + -
312A ALA 2.8 17.5 + - - +
313A ILE* 3.1 10.3 + - - +
315A GLU* 1.3 73.0 - - - +
317A PHE* 1.3 62.3 + - + +
318A GLU 3.1 0.2 - - - -
319A MET* 3.1 29.8 + - - +
322A ILE* 3.5 35.5 - - + +
338A THR* 4.0 9.6 - - + -
341A LEU* 3.8 29.8 - - + -
342A PHE* 4.0 40.6 - - + +
345A VAL* 4.3 7.4 - - + -
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Residues in contact with PHE 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LYS* 4.0 20.6 - - + -
27A VAL* 3.7 24.2 - - + -
58A ILE* 3.7 32.1 - - + -
88A TYR* 3.7 32.8 - + - -
313A ILE* 3.1 34.3 + - + +
314A HIS 3.3 5.8 + - - +
315A GLU 3.3 0.2 - - - -
316A LEU* 1.3 79.3 - - + +
318A GLU* 1.3 56.9 + - - +
319A MET 3.1 12.1 - - - +
322A ILE* 3.8 25.4 - - + -
324A ASP* 5.7 0.2 - - - -
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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
------------------------------------------------------------
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