Contacts of the helix formed by residues 25 - 46 (chain D) in PDB entry 5A31
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 VAL 25 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PRO* 3.5 2.4 - - - +
24D CYS* 1.3 82.7 - - + +
26D GLU* 1.3 63.1 + - - +
27D GLU* 3.1 9.2 - - + +
28D THR* 2.7 59.9 + - + +
29D GLU* 3.2 8.2 + - - +
439I LYS* 5.0 15.3 - - + +
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Residues in contact with GLU 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PRO* 3.9 23.1 + - + +
24D CYS 3.2 5.0 + - - +
25D VAL* 1.3 73.4 - - - +
27D GLU* 1.3 54.2 + - - +
29D GLU* 3.3 20.7 + - - +
30D LEU* 2.8 34.8 + - + +
442I GLN* 4.2 15.8 - - - +
134O LEU* 3.4 28.6 - - - +
138O HIS* 3.6 28.0 + - - +
210O LYS* 4.3 23.8 + - - +
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Residues in contact with GLU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24D CYS 4.9 0.8 + - - -
25D VAL* 3.1 7.1 - - + +
26D GLU* 1.3 79.7 + - - +
28D THR* 1.3 73.0 + - + +
30D LEU* 3.4 8.0 + - - +
31D GLN* 3.0 33.1 + - - +
427I ARG* 5.0 5.9 + - - -
129O THR* 4.4 20.0 - - + +
134O LEU* 4.1 36.1 - - + +
137O ARG* 4.6 8.0 + - - +
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Residues in contact with THR 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D VAL* 2.7 44.1 + - + +
27D GLU* 1.3 93.4 - - - +
29D GLU* 1.3 60.1 + - - +
31D GLN* 3.4 19.0 + - - +
32D GLN* 2.9 26.5 + - - +
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Residues in contact with GLU 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23D PRO* 4.6 11.1 - - + +
25D VAL 3.2 12.3 + - - +
26D GLU* 3.6 25.0 - - - +
28D THR* 1.3 73.8 + - - +
30D LEU* 1.3 64.3 + - - +
32D GLN* 3.1 18.5 + - - +
33D GLN* 3.0 35.3 + - + +
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Residues in contact with LEU 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D GLU* 2.8 21.3 + - + +
27D GLU* 3.6 6.5 - - - +
29D GLU* 1.3 72.2 + - - +
31D GLN* 1.3 58.7 + - - +
33D GLN* 3.2 15.7 + - - +
34D GLU* 2.8 33.3 + - + +
134O LEU* 4.4 8.7 - - + +
137O ARG* 3.1 51.1 - - + +
138O HIS* 3.4 61.7 - - + +
141O LEU* 5.0 7.6 - - + +
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Residues in contact with GLN 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D GLU* 3.0 21.3 + - - +
28D THR* 3.5 23.6 - - - +
29D GLU 3.2 0.2 - - - -
30D LEU* 1.3 80.9 - - - +
32D GLN* 1.3 59.8 + - - +
34D GLU* 3.5 18.4 - - - +
35D GLN* 2.8 38.5 + - + +
137O ARG* 4.4 9.2 - - - +
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Residues in contact with GLN 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D THR 2.9 13.9 + - - +
29D GLU* 3.1 19.9 + - - +
31D GLN* 1.3 80.7 + - - +
33D GLN* 1.3 59.4 + - - +
35D GLN* 3.6 14.4 - - + +
36D GLN* 2.9 51.2 + - + +
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Residues in contact with GLN 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D GLU* 3.0 23.6 + - + +
30D LEU* 3.2 20.8 + - - +
32D GLN* 1.3 73.6 - - - +
34D GLU* 1.3 67.8 + - - +
36D GLN* 3.1 11.2 + - - +
37D HIS* 2.9 25.6 + - - +
27O LYS 5.2 9.7 - - - +
138O HIS* 5.5 5.4 + - - -
141O LEU* 3.9 21.4 - - + +
145O LYS* 4.7 13.6 + - - +
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Residues in contact with GLU 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D LEU* 2.8 25.9 + - + +
31D GLN* 3.5 21.2 - - - +
33D GLN* 1.3 74.1 - - - +
35D GLN* 1.3 64.0 + - - +
37D HIS* 3.6 5.0 + - - +
38D GLN* 3.4 24.0 + - + +
128O LYS* 5.2 1.4 - - - -
137O ARG* 2.7 42.4 + - + +
141O LEU* 4.1 20.9 - - + +
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Residues in contact with GLN 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D GLN* 2.8 32.5 + - + +
32D GLN* 3.6 16.6 + - - +
34D GLU* 1.3 75.5 - - - +
36D GLN* 1.3 77.3 + - - +
38D GLN* 3.2 12.3 + - + +
39D ALA* 3.0 28.9 + - - +
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Residues in contact with GLN 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D GLN* 2.9 42.9 + - + +
33D GLN* 3.1 11.1 + - - +
35D GLN* 1.3 85.5 - - - +
37D HIS* 1.3 65.8 + - - +
39D ALA* 3.1 9.3 + - + +
40D TRP* 3.0 22.2 + - - +
145O LYS* 6.1 1.1 - - - +
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Residues in contact with HIS 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33D GLN 2.9 16.3 + - - +
34D GLU 3.6 6.2 + - - +
36D GLN* 1.3 75.8 - - - +
38D GLN* 1.3 63.3 + - - +
40D TRP* 3.2 27.7 + + - +
41D LEU* 3.1 51.3 + - + +
141O LEU* 4.1 15.1 - - + +
144O SER* 3.8 38.4 + - - -
145O LYS* 3.8 33.8 - - + +
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Residues in contact with GLN 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34D GLU* 3.4 15.6 + - + +
35D GLN* 3.2 13.2 + - + +
37D HIS* 1.3 82.1 + - - +
39D ALA* 1.3 65.0 + - - +
41D LEU* 3.2 29.5 + - - +
42D GLN* 2.9 34.2 + - - +
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Residues in contact with ALA 39 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D GLN* 3.0 18.7 + - - +
36D GLN* 3.1 13.9 + - + +
38D GLN* 1.3 75.8 - - - +
40D TRP* 1.3 58.2 + - - +
42D GLN* 3.2 16.3 + - - +
43D SER* 2.9 26.3 + - - -
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Residues in contact with TRP 40 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D GLN 3.0 11.6 + - - +
37D HIS* 3.5 29.8 - + - +
39D ALA* 1.3 74.9 - - - +
41D LEU* 1.3 96.6 + - + +
43D SER* 3.3 11.9 + - - -
44D ILE* 3.2 43.8 + - + +
349P LYS* 4.6 14.4 - - + -
352P LEU* 3.5 27.8 - - + -
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Residues in contact with LEU 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D HIS* 3.1 36.8 + - + +
38D GLN* 3.2 30.2 + - - +
40D TRP* 1.3 104.8 - - + +
42D GLN* 1.3 59.3 + - - +
44D ILE* 3.3 5.6 + - + +
45D ALA* 2.8 28.6 + - - +
348P GLU* 3.2 43.9 - - + +
349P LYS* 5.4 5.6 - - + +
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Residues in contact with GLN 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLN* 2.9 27.9 + - - +
39D ALA* 3.2 13.1 + - - +
41D LEU* 1.3 72.4 - - - +
43D SER* 1.3 56.0 + - - +
45D ALA* 3.9 7.6 - - + -
46D GLU* 2.7 48.0 + - + +
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Residues in contact with SER 43 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D ALA 2.9 16.0 + - - -
40D TRP* 3.3 18.2 + - - -
42D GLN* 1.3 71.4 - - - +
44D ILE* 1.3 64.3 + - - +
46D GLU* 3.2 5.4 - - - +
47D LYS* 3.1 42.5 + - - +
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Residues in contact with ILE 44 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40D TRP* 3.2 61.4 + - + +
41D LEU* 4.0 10.8 - - + +
43D SER* 1.3 78.1 - - - +
45D ALA* 1.3 60.8 + - - +
47D LYS* 3.6 17.1 - - + +
348P GLU* 4.0 22.0 - - - +
351P ALA* 4.4 7.4 - - + -
352P LEU* 3.7 23.1 - - + -
355P GLN* 4.3 21.1 - - - +
375P TYR* 3.5 19.1 - - - -
378P MET* 4.3 2.2 - - - +
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Residues in contact with ALA 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41D LEU 2.8 17.9 + - - +
42D GLN* 3.4 7.6 - - + +
44D ILE* 1.3 79.4 - - - +
46D GLU* 1.3 79.5 + - - +
47D LYS 3.5 0.2 - - - -
348P GLU* 3.4 13.7 - - - +
375P TYR* 4.2 0.3 - - - -
378P MET* 3.5 26.1 - - + +
380P ASN* 2.9 23.6 + - - +
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Residues in contact with GLU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42D GLN* 2.7 29.4 + - + +
43D SER* 3.2 8.4 - - - +
45D ALA* 1.3 95.2 - - + +
47D LYS* 1.3 63.4 + - - +
48D ASP 3.4 2.6 + - - -
49D ASN* 3.8 33.5 + - + +
378P MET 4.3 7.6 - - - +
379P LYS 5.1 0.5 - - - -
380P ASN* 3.3 23.3 - - - +
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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