Contacts of the helix formed by residues 26 - 45 (chain A) in PDB entry 3CWL
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 ILE 26 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A ASN* 3.1 16.5 - - - +
25A LYS* 1.3 78.4 - - + +
27A THR* 1.3 65.6 + - - +
28A PRO* 3.3 3.1 - - - -
29A ASN* 3.1 12.1 + - - +
30A LEU* 3.0 35.3 + - + +
82A PHE* 3.8 14.1 - - + -
87A ILE* 4.4 4.7 - - + -
91A GLN 3.7 23.3 - - - +
92A ILE* 3.8 15.5 - - - +
95A GLY* 3.7 6.7 - - - +
96A PHE* 3.6 58.3 - - + +
99A LEU* 4.9 2.0 - - + -
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Residues in contact with THR 27 (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* 3.9 8.7 - - + -
24A ASN* 3.4 22.9 + - - +
26A ILE* 1.3 78.4 - - - +
28A PRO* 1.4 61.1 - - + +
30A LEU* 3.3 11.4 + - - +
31A ALA* 3.0 26.7 + - - +
269A HIS* 3.6 21.3 - - + +
379A THR 2.5 26.5 + - - +
380A LYS 3.4 23.1 - - - +
381A SER* 3.7 10.9 + - - +
382A PRO* 4.7 1.1 - - + +
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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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23A PHE* 4.5 16.6 - - + -
24A ASN 3.8 5.6 - - - +
25A LYS 3.6 13.7 - - - +
26A ILE 3.4 5.2 - - - -
27A THR* 1.4 94.7 - - + +
29A ASN* 1.3 59.5 + - - +
31A ALA* 3.3 3.3 + - - +
32A GLU* 3.0 33.7 + - - +
269A HIS* 4.3 21.2 - - + +
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Residues in contact with ASN 29 (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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25A LYS 3.8 15.1 - - - +
26A ILE 3.1 10.5 + - - +
28A PRO* 1.3 76.1 - - - +
30A LEU* 1.3 60.5 + - - +
32A GLU* 3.3 3.6 + - - -
33A PHE* 2.8 30.1 + - - +
80A LEU 4.3 2.5 - - - +
81A ASN* 2.7 34.4 + - - +
82A PHE* 3.6 38.1 - - + +
83A ASN 4.6 2.8 - - - +
87A ILE* 4.8 7.9 - - - +
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Residues in contact with LEU 30 (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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26A ILE* 3.0 30.7 + - + +
27A THR* 3.5 10.3 - - - +
29A ASN* 1.3 75.9 - - - +
31A ALA* 1.3 56.2 + - - +
33A PHE* 3.2 7.7 + - + +
34A ALA* 2.9 29.3 + - - +
54A PRO* 4.1 11.8 - - + +
55A VAL* 4.3 9.0 - - + -
58A ALA* 3.6 32.1 - - + -
80A LEU 5.4 0.7 - - - +
82A PHE* 5.6 1.8 - - + -
96A PHE* 4.0 10.1 - - + -
99A LEU* 3.6 20.4 - - + -
381A SER* 3.5 27.8 - - - +
382A PRO* 3.8 12.4 - - + +
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Residues in contact with ALA 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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27A THR 3.0 16.3 + - - +
28A PRO 3.6 4.0 - - - +
29A ASN 3.3 0.2 - - - -
30A LEU* 1.3 74.8 - - - +
32A GLU* 1.3 62.4 + - - +
34A ALA* 3.4 3.6 + - - +
35A PHE* 3.1 36.8 + - + -
269A HIS* 3.6 40.2 - - + +
382A PRO* 4.0 15.1 - - + +
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Residues in contact with GLU 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 19.7 + - - +
29A ASN* 3.3 6.0 + - - +
31A ALA* 1.3 76.5 - - - +
33A PHE* 1.3 58.6 + - - +
35A PHE* 3.5 27.9 + - - +
36A SER* 2.9 34.1 + - - -
39A ARG* 5.0 4.7 + - - -
81A ASN* 3.9 17.7 - - + +
268A THR* 5.3 3.3 - - - +
269A HIS* 4.6 9.7 + - - +
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Residues in contact with PHE 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 ASN 2.8 17.6 + - - +
30A LEU* 3.4 7.0 - - + +
32A GLU* 1.3 74.3 - - - +
34A ALA* 1.3 61.3 + - - +
36A SER* 3.1 1.4 + - - -
37A LEU* 2.9 55.4 + - + +
54A PRO* 3.7 34.3 - - + -
57A ILE* 3.8 17.9 - - + -
58A ALA* 4.1 7.9 - - + -
79A GLY 3.6 9.4 - - - -
80A LEU* 3.6 34.5 - - + +
81A ASN* 3.1 25.7 - - - +
303A LEU* 3.9 5.2 - - + -
306A LEU* 3.7 24.5 - - + -
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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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30A LEU 2.9 12.3 + - - +
31A ALA* 3.4 10.3 - - - +
33A PHE* 1.3 76.6 - - - +
35A PHE* 1.3 60.3 + - + +
38A TYR* 2.8 32.6 + - - +
52A PHE* 3.5 7.3 - - - -
54A PRO* 3.5 31.4 - - + -
373A LEU* 5.2 0.7 - - + -
382A PRO* 4.0 13.7 - - + -
385A MET* 4.3 12.8 - - + -
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Residues in contact with PHE 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 ALA* 3.1 24.7 + - + +
32A GLU* 3.6 25.4 - - - +
33A PHE 3.3 0.2 - - - -
34A ALA* 1.3 76.5 - - + +
36A SER* 1.3 57.7 + - - +
38A TYR* 3.8 3.1 - - - +
39A ARG* 2.8 61.8 + - - +
267A LEU* 4.1 24.9 - - + -
268A THR* 3.6 25.1 - - - -
269A HIS* 3.4 26.0 - - + -
272A ILE* 4.7 8.7 - - + -
373A LEU* 4.6 10.1 - - + -
385A MET* 4.1 26.0 - - + -
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Residues in contact with SER 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 GLU* 2.9 21.0 + - - +
33A PHE 3.6 3.6 - - - -
35A PHE* 1.3 76.4 - - - +
37A LEU* 1.3 57.4 + - - +
39A ARG* 4.0 5.6 - - - +
40A GLN* 3.1 27.5 + - - +
81A ASN* 3.5 19.8 + - - -
306A LEU* 3.7 22.2 - - - +
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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 PHE* 2.9 42.8 + - + +
34A ALA 4.1 1.8 - - - +
36A SER* 1.3 74.2 - - - +
38A TYR* 1.3 65.9 + - - +
40A GLN* 3.3 4.8 + - + +
41A LEU* 2.9 40.2 + - + +
52A PHE* 4.0 17.7 - - + -
57A ILE* 3.7 26.5 - - + -
297A TYR* 6.3 0.2 - - + -
299A LEU* 5.2 0.9 - - + -
302A VAL* 3.0 35.2 - - + -
303A LEU* 4.3 8.3 - - + -
306A LEU* 4.0 14.6 - - + +
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Residues in contact with TYR 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 2.8 19.8 + - - +
35A PHE* 3.8 3.4 - + - +
37A LEU* 1.3 76.1 - - - +
39A ARG* 1.3 61.7 + - + +
41A LEU* 3.1 6.5 + - - +
42A ALA* 2.7 40.0 + - + -
50A ILE* 4.0 24.5 - - + -
52A PHE* 3.7 11.5 - + + -
264A GLU* 2.4 49.5 + - + -
267A LEU* 6.4 0.2 - - + -
371A VAL* 3.5 11.8 - - + +
385A MET* 3.6 38.6 - - + -
386A GLY 4.0 23.6 - - - -
387A LYS* 3.4 20.6 - - + +
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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
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32A GLU* 5.0 5.1 + - - -
35A PHE* 2.8 49.4 + - - +
36A SER* 4.0 6.1 - - - +
38A TYR* 1.3 83.8 - - + +
40A GLN* 1.3 56.4 + - - +
42A ALA* 3.8 4.8 - - + +
43A HIS* 3.0 30.5 + - - +
264A GLU* 2.7 33.9 + - + +
265A ASN* 3.3 18.6 + - - +
267A LEU* 3.1 29.1 + - - +
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Residues in contact with GLN 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 SER 3.1 19.0 + - - +
37A LEU* 3.4 9.9 - - + +
39A ARG* 1.3 75.7 - - - +
41A LEU* 1.3 57.5 + - - +
43A HIS* 3.2 15.4 + - - +
44A GLN* 3.0 51.7 + - - +
302A VAL* 4.6 11.7 - - + +
305A GLN* 3.6 48.5 + - + +
306A LEU* 4.6 9.0 - - + +
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Residues in contact with LEU 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 26.3 + - + +
38A TYR 3.4 6.3 - - - +
40A GLN* 1.3 76.0 - - - +
42A ALA* 1.3 61.0 + - - +
44A GLN* 3.4 26.2 + - - +
45A SER* 3.4 20.6 + - - +
48A THR* 5.5 0.7 + - - -
50A ILE* 3.7 23.9 - - + +
52A PHE* 3.6 32.5 - - + -
297A TYR* 3.6 42.0 - - + -
302A VAL* 4.1 17.7 - - + -
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Residues in contact with ALA 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 TYR* 2.7 38.2 + - + +
39A ARG* 3.8 7.4 - - + +
41A LEU* 1.3 70.7 - - - +
43A HIS* 1.3 61.4 + - - +
45A SER 3.1 12.0 - - - +
46A ASN* 2.6 28.6 - - - +
50A ILE* 3.8 9.2 - - + +
261A GLN* 6.0 0.7 - - - +
264A GLU* 4.2 17.7 - - + +
387A LYS* 4.4 2.9 - - - +
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Residues in contact with HIS 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 3.0 18.3 + - - +
40A GLN* 3.4 16.2 + - - +
42A ALA* 1.3 76.8 - - - +
44A GLN* 1.3 63.4 + - - +
45A SER* 3.5 1.0 + - - -
46A ASN* 4.9 3.2 + - - +
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Residues in contact with GLN 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 GLN* 3.0 41.1 + - - +
41A LEU* 3.6 28.8 + - - +
42A ALA 3.3 0.4 - - - -
43A HIS* 1.3 78.9 - - - +
45A SER* 1.3 60.8 - - - +
297A TYR* 6.0 0.4 - - - -
301A SER* 5.2 3.7 + - - -
302A VAL* 4.3 18.2 - - - +
305A GLN* 4.6 8.3 - - - +
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Residues in contact with SER 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 LEU 3.4 10.9 + - - +
42A ALA* 3.1 18.3 - - - +
43A HIS 3.3 1.7 - - - -
44A GLN* 1.3 81.3 - - - +
46A ASN* 1.3 63.2 + - - +
47A SER* 3.2 15.8 + - - -
48A THR* 3.7 31.9 + - - +
50A ILE* 4.6 5.2 - - - +
387A LYS* 4.9 0.9 + - - -
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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
------------------------------------------------------------
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