Contacts of the helix formed by residues 27 - 45 (chain A) in PDB entry 5E2Q
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 SER 27 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A LEU 3.6 2.0 + - - -
26A LEU* 1.3 75.0 - - - +
28A PRO* 1.3 69.5 - - - +
29A THR* 3.6 7.1 + - - -
30A GLU* 2.8 40.1 + - - +
31A ARG* 2.8 28.1 + - - +
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Residues in contact with PRO 28 (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 SER* 1.3 87.1 - - - +
29A THR* 1.3 58.5 + - - +
31A ARG* 3.4 22.5 + - + +
32A LEU* 3.0 39.0 + - + +
682A SER 5.5 3.8 - - - +
684A VAL* 5.3 0.3 - - - +
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Residues in contact with THR 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A SER* 3.2 6.3 + - - -
28A PRO* 1.3 78.0 - - - +
30A GLU* 1.3 62.6 + - + +
32A LEU* 3.3 10.5 + - - +
33A TYR* 2.9 27.5 + - - +
268A TYR* 3.6 38.4 - - + +
269A ALA 5.5 1.1 - - - +
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU 4.3 2.1 - - - +
26A LEU* 3.3 20.1 - - + +
27A SER* 2.8 39.3 + - - +
29A THR* 1.3 77.6 - - + +
31A ARG* 1.3 57.9 + - - +
33A TYR* 3.3 9.1 + - + +
34A ALA* 3.0 28.2 + - - +
270A ALA* 6.4 2.2 - - + -
307A ILE* 3.4 39.6 - - + +
308A VAL* 4.2 10.9 - - + +
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Residues in contact with ARG 31 (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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23A PHE* 3.2 58.2 + - + -
24A ARG* 4.2 12.9 + - - +
26A LEU* 3.1 37.7 + - + -
27A SER 2.8 18.6 + - - +
28A PRO* 3.6 22.8 - - + +
30A GLU* 1.3 74.3 - - - +
32A LEU* 1.3 59.5 + - - +
34A ALA* 3.2 3.3 + - - +
35A TYR* 2.8 30.1 + - - +
677A THR* 6.0 0.2 - - - +
684A VAL* 3.7 31.7 + - + +
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Residues in contact with LEU 32 (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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28A PRO* 3.0 26.2 + - + +
29A THR* 3.3 6.7 + - - +
31A ARG* 1.3 76.2 - - - +
33A TYR* 1.3 62.2 + - - +
35A TYR* 3.6 5.1 - - + +
36A HIS* 3.1 36.8 + - - +
268A TYR* 3.5 44.2 - - + +
679A LEU* 3.6 37.5 - - + -
681A GLY 5.5 1.1 - - - +
682A SER* 4.1 13.5 - - - +
684A VAL* 3.8 8.3 - - + -
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Residues in contact with TYR 33 (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 THR 2.9 17.3 + - - +
30A GLU* 3.4 8.7 - - + +
32A LEU* 1.3 79.0 - - - +
34A ALA* 1.3 60.5 + - - +
37A LEU* 3.2 50.7 + - + +
265A ALA* 3.4 26.4 - - - +
268A TYR* 3.7 22.6 - - - +
269A ALA* 4.0 7.0 - - + -
270A ALA 5.8 0.2 - - - -
274A GLN* 3.6 28.4 + - - +
277A MET* 3.7 24.9 - - - +
278A LEU* 4.2 12.7 - - + +
308A VAL* 3.8 40.8 + - + -
310A SER* 4.0 1.6 + - - -
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Residues in contact with ALA 34 (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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23A PHE* 6.1 1.8 - - + -
26A LEU* 4.5 6.5 - - + -
30A GLU 3.0 16.1 + - - +
31A ARG* 3.2 4.7 + - - +
33A TYR* 1.3 74.6 - - - +
35A TYR* 1.3 57.5 + - - +
37A LEU* 4.0 1.0 - - - +
38A SER* 2.7 38.7 + - - +
308A VAL* 4.3 8.3 - - + -
332A VAL* 3.8 25.3 - - + +
379A LEU* 4.2 17.9 - - + -
677A THR* 5.2 4.3 - - + -
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Residues in contact with TYR 35 (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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31A ARG 2.8 17.7 + - - +
32A LEU* 3.6 9.2 - - + +
33A TYR 3.2 0.2 - - - -
34A ALA* 1.3 78.1 - - - +
36A HIS* 1.3 97.1 + + - +
38A SER* 3.6 3.1 + - - -
39A ARG* 3.2 61.2 + - + +
677A THR* 3.2 46.6 + - - +
678A ARG* 4.2 3.2 - - - -
679A LEU* 3.6 45.1 + - + +
684A VAL* 4.3 10.1 - - + -
706A GLU* 4.4 8.8 + - - -
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Residues in contact with HIS 36 (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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32A LEU* 3.1 26.1 + - - +
35A TYR* 1.3 99.6 - + - +
37A LEU* 1.3 62.2 + - - +
39A ARG* 3.3 2.4 + - - -
40A ALA* 3.0 23.4 + - - +
261A GLN* 3.0 51.4 + - - +
264A LYS* 3.8 28.0 - - + +
265A ALA* 3.7 9.2 - - + -
268A TYR* 3.7 30.6 + + - -
679A LEU* 4.6 11.2 - - + +
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Residues in contact with LEU 37 (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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33A TYR* 3.2 47.8 + - + +
34A ALA 4.0 1.6 - - - +
36A HIS* 1.3 78.9 - - - +
38A SER* 1.3 58.0 + - - +
40A ALA* 3.2 5.3 + - - +
41A ALA* 2.9 27.2 + - - +
262A LEU* 3.7 28.5 - - + -
265A ALA* 3.9 15.9 - - + -
278A LEU* 4.0 12.8 - - + -
310A SER* 3.4 33.2 - - - +
312A ILE* 5.2 3.8 - - + +
332A VAL* 3.6 18.1 - - + +
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Residues in contact with SER 38 (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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34A ALA* 2.7 25.5 + - - +
35A TYR 3.7 4.9 - - - -
37A LEU* 1.3 77.0 - - - +
39A ARG* 1.3 57.1 + - - +
41A ALA* 3.1 3.2 + - - +
42A TRP* 2.8 40.4 + - - -
332A VAL* 3.6 15.3 - - - +
379A LEU* 5.1 3.3 - - - +
380A THR* 3.2 31.8 + - - -
677A THR* 4.4 14.7 + - - +
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Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A TYR* 3.2 53.4 + - + +
36A HIS* 3.3 9.2 + - - +
38A SER* 1.3 77.5 - - - +
40A ALA* 1.3 56.6 + - - +
42A TRP* 4.1 7.0 - - + +
43A TYR* 2.6 70.3 + - + -
261A GLN* 3.5 35.2 + - + +
264A LYS* 5.5 3.0 - - - +
677A THR* 5.6 1.6 - - - +
703A ARG 5.8 4.6 + - - +
704A PHE* 5.2 1.0 - - - -
706A GLU* 3.4 38.3 + - - +
707A ASP* 4.4 1.0 + - - -
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Residues in contact with ALA 40 (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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36A HIS 3.0 12.6 + - - +
37A LEU 3.4 9.6 - - - +
39A ARG* 1.3 76.5 - - - +
41A ALA* 1.3 62.3 + - - +
43A TYR* 3.6 5.0 - - - +
44A GLY* 3.1 19.2 + - - -
258A VAL* 3.6 35.4 - - + +
261A GLN* 3.7 9.1 - - + +
262A LEU* 3.9 22.4 - - + +
312A ILE* 4.0 6.0 - - + +
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Residues in contact with ALA 41 (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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37A LEU 2.9 13.0 + - - +
38A SER* 3.1 8.7 + - - +
40A ALA* 1.3 77.5 - - - +
42A TRP* 1.3 56.9 + - - +
44A GLY 3.4 0.5 + - - -
45A GLY 2.8 25.5 + - - -
312A ILE* 4.1 11.8 - - + +
328A PHE* 4.5 3.1 - - - -
330A GLY* 3.7 32.3 - - - +
331A PHE* 4.6 1.3 - - - +
332A VAL* 5.1 2.0 - - + -
380A THR* 4.0 14.1 - - + -
382A ALA* 3.2 11.0 - - + +
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Residues in contact with TRP 42 (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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38A SER* 2.8 35.0 + - - +
39A ARG* 4.1 6.3 - - + +
41A ALA* 1.3 69.8 - - - +
43A TYR* 1.3 67.2 + - - +
45A GLY* 3.5 7.3 + - - -
46A LEU* 3.7 8.3 + - - +
380A THR* 3.2 32.5 + - + -
381A PHE 4.2 2.7 - - - -
382A ALA* 3.7 21.3 - - + -
383A GLY 5.1 1.3 - - - -
674A GLN* 3.6 36.1 - - + -
675A PRO 4.6 2.3 + - - -
676A ASN* 4.3 6.2 + - - +
700A PHE* 4.2 15.5 - + - -
703A ARG* 3.3 58.5 - - + +
704A PHE* 3.5 33.2 - + + -
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Residues in contact with TYR 43 (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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39A ARG* 2.6 55.6 + - - +
40A ALA* 3.6 5.4 - - - +
42A TRP* 1.3 77.0 - - - +
44A GLY* 1.3 62.0 + - - +
46A LEU* 3.1 20.0 + - - +
254A ILE* 3.3 16.9 - - + +
257A LYS* 3.3 39.8 - - + +
258A VAL* 3.9 9.2 - - + -
260A GLU* 5.6 0.2 - - - -
261A GLN* 3.6 24.2 + - + -
704A PHE* 4.0 12.1 - + - -
707A ASP* 2.7 34.5 + - - -
711A LEU* 3.8 31.4 - - + -
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Residues in contact with GLY 44 (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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40A ALA 3.1 7.3 + - - -
43A TYR* 1.3 74.4 - - - +
45A GLY* 1.3 59.3 + - - +
46A LEU 3.0 2.9 - - - -
47A ALA* 3.0 24.9 + - - +
254A ILE* 4.0 7.4 - - - -
255A LEU* 5.5 0.9 - - - -
258A VAL* 3.5 14.9 - - - +
328A PHE* 3.2 38.4 - - - +
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Residues in contact with GLY 45 (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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41A ALA 2.8 17.6 + - - -
42A TRP* 3.5 4.7 + - - -
43A TYR 3.1 0.8 - - - -
44A GLY* 1.3 76.6 - - - +
46A LEU* 1.3 59.5 + - - +
48A VAL* 3.2 23.9 + - - +
103A MET* 3.3 19.6 - - - +
328A PHE* 4.0 4.2 - - - -
329A GLU* 5.9 0.2 - - - -
382A ALA* 4.2 12.8 - - - -
383A GLY* 4.3 7.4 - - - -
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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
------------------------------------------------------------
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