Contacts of the helix formed by residues 25 - 50 (chain B) in PDB entry 4Y2H
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 25 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B SER* 1.3 77.9 - - - +
26B ALA* 1.3 62.9 + - - +
28B GLU* 3.4 16.7 + - - +
29B ARG* 3.1 40.4 + - - +
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B SER 3.6 7.5 - - - +
25B ILE* 1.3 81.5 - - - +
27B ALA* 1.3 61.0 + - - +
29B ARG* 3.4 11.0 + - - +
30B GLU* 3.2 26.4 + - - +
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B SER* 3.5 22.1 - - - +
25B ILE 3.3 0.6 - - - -
26B ALA* 1.3 79.0 - - - +
28B GLU* 1.3 57.6 + - + +
30B GLU* 3.3 10.3 + - - +
31B ALA* 3.0 25.7 + - - +
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B SER* 3.0 26.7 + - - +
25B ILE* 3.4 23.0 - - - +
27B ALA* 1.3 73.4 - - + +
29B ARG* 1.3 61.0 + - + +
31B ALA* 3.3 8.7 + - - +
32B ALA* 3.0 27.4 + - - +
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Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ILE* 3.1 38.0 + - + +
26B ALA* 3.6 10.0 - - - +
27B ALA 3.3 0.2 - - - -
28B GLU* 1.3 74.3 - - + +
30B GLU* 1.3 65.8 + - - +
32B ALA* 3.3 16.4 + - - +
33B LEU* 3.4 22.4 + - + +
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Residues in contact with GLU 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ALA 3.2 13.8 + - - +
27B ALA* 3.3 11.2 + - - +
29B ARG* 1.3 78.4 - - - +
31B ALA* 1.3 61.8 + - - +
33B LEU* 3.3 8.4 + - - +
34B GLU* 3.2 24.7 + - - +
37B ARG* 2.9 33.1 + - - +
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Residues in contact with ALA 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ALA 3.0 14.7 + - - +
28B GLU* 3.6 12.6 - - - +
29B ARG 3.3 0.4 - - - -
30B GLU* 1.3 75.6 - - - +
32B ALA* 1.3 61.2 + - - +
34B GLU* 3.7 19.4 + - - +
35B ARG* 4.7 2.1 + - - +
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B GLU 3.0 13.3 + - - +
29B ARG* 3.4 13.7 - - - +
30B GLU 3.2 0.4 - - - -
31B ALA* 1.3 79.6 - - - +
33B LEU* 1.3 64.1 + - + +
34B GLU 3.6 0.7 + - - -
35B ARG* 4.6 2.3 + - - +
36B PRO* 3.8 12.1 - - - +
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Residues in contact with LEU 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ARG* 3.4 17.7 + - + +
30B GLU* 3.3 8.5 + - - +
32B ALA* 1.3 77.5 - - + +
34B GLU* 1.3 65.0 + - - +
35B ARG 3.4 1.6 - - - -
36B PRO* 3.3 14.4 - - + +
37B ARG* 3.1 70.3 + - + +
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Residues in contact with GLU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLU 3.2 14.4 + - - +
31B ALA* 3.7 15.2 + - - +
32B ALA 3.4 2.0 - - - -
33B LEU* 1.3 77.7 - - - +
35B ARG* 1.3 64.0 + - - +
37B ARG* 3.4 9.7 + - - +
38B ARG* 3.0 35.5 + - - +
41B ARG* 4.0 25.8 + - - -
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Residues in contact with ARG 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B ALA 4.7 2.3 + - - +
32B ALA 4.6 2.8 + - - +
34B GLU* 1.3 78.4 - - - +
36B PRO* 1.4 68.2 - - + +
38B ARG* 3.3 34.1 + - - +
39B THR* 2.8 30.0 + - - +
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Residues in contact with PRO 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA 3.8 9.0 - - - +
33B LEU* 3.3 34.1 - - + +
35B ARG* 1.4 94.1 - - + +
37B ARG* 1.3 59.4 + - + +
39B THR* 3.4 8.4 + - - +
40B LYS* 3.1 24.1 + - - +
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Residues in contact with ARG 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B GLU* 2.9 36.4 + - - -
33B LEU* 3.1 57.2 + - + +
34B GLU* 3.7 12.3 - - - +
36B PRO* 1.3 76.3 - - + +
38B ARG* 1.3 56.8 + - - +
40B LYS* 3.7 6.5 + - - +
41B ARG* 3.2 42.6 + - - +
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Residues in contact with ARG 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B GLU* 3.0 26.6 + - - +
35B ARG* 3.8 40.9 + - - +
36B PRO 3.2 0.2 - - - -
37B ARG* 1.3 73.7 - - - +
39B THR* 1.3 62.6 + - - +
40B LYS 3.2 0.2 - - - -
41B ARG* 3.2 26.9 + - - +
42B GLU* 2.8 59.0 + - + +
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Residues in contact with THR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ARG* 2.8 21.5 + - - +
36B PRO* 3.7 10.9 - - - +
38B ARG* 1.3 79.4 + - - +
40B LYS* 1.3 56.7 + - - +
42B GLU* 3.4 14.6 + - - +
43B ARG* 2.9 60.6 + - + +
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Residues in contact with LYS 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B PRO 3.1 16.6 + - - +
37B ARG* 3.9 7.0 - - - +
38B ARG 3.2 0.2 - - - -
39B THR* 1.3 74.5 - - - +
41B ARG* 1.3 55.8 + - + +
43B ARG* 3.2 11.3 + - + +
44B ASP* 2.8 57.0 + - - +
350B PRO* 6.5 1.1 - - + -
351B ARG* 5.6 2.2 - - - +
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Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34B GLU* 4.0 17.8 + - - -
37B ARG* 3.2 31.6 + - - +
38B ARG* 3.5 36.5 - - - +
40B LYS* 1.3 77.9 - - + +
42B GLU* 1.3 63.6 + - + +
44B ASP* 3.4 8.3 + - - +
45B GLN* 3.0 24.5 + - - +
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Residues in contact with GLU 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ARG* 2.8 47.1 + - + +
39B THR* 3.6 13.9 + - - +
41B ARG* 1.3 76.2 - - + +
43B ARG* 1.3 62.4 + - - +
45B GLN* 3.3 7.7 + - - +
46B LEU* 3.2 29.5 + - + +
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Residues in contact with ARG 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B THR* 2.9 44.0 + - + +
40B LYS* 3.2 10.0 + - + +
42B GLU* 1.3 76.8 - - + +
44B ASP* 1.3 64.5 + - - +
46B LEU* 3.1 23.0 + - + +
47B TYR* 3.1 13.1 + - - +
347B ARG 5.4 1.4 + - - -
348B ASP* 3.3 26.8 + - - +
349B ASN* 5.3 7.0 - - - +
350B PRO* 3.7 27.9 - - + +
351B ARG* 5.3 4.2 - - + +
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Residues in contact with ASP 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LYS* 2.8 49.7 + - - +
41B ARG* 3.7 7.8 + - - +
43B ARG* 1.3 73.7 - - - +
45B GLN* 1.3 57.7 + - - +
47B TYR* 3.3 1.8 + - - +
48B TYR* 2.9 58.4 + - + +
351B ARG* 3.0 38.8 + - - +
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Residues in contact with GLN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ARG 3.0 18.2 + - - +
42B GLU* 3.5 8.5 - - - +
43B ARG 3.1 0.2 - - - -
44B ASP* 1.3 76.8 - - - +
46B LEU* 1.3 65.7 + - + +
48B TYR* 3.5 15.3 + - + +
49B GLU* 2.7 54.5 + - - +
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Residues in contact with LEU 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B GLU* 3.2 17.3 + - + +
43B ARG* 3.1 15.7 + - + +
45B GLN* 1.3 77.5 - - - +
47B TYR* 1.3 65.5 + - - +
49B GLU* 3.4 26.9 + - - +
50B CYS* 3.4 15.1 + - - -
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Residues in contact with TYR 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B ARG 3.1 9.0 + - - +
44B ASP 3.6 4.9 - - - +
46B LEU* 1.3 75.3 - - - +
48B TYR* 1.3 78.6 + + - +
50B CYS* 2.9 29.3 + - - +
51B TYR* 3.7 20.7 - + - -
164B GLU* 2.7 54.7 + - + +
166B MET* 4.1 9.9 - - - +
351B ARG* 3.5 50.3 - - + +
401B SAH 3.7 31.2 - + - -
402B 49K 4.3 9.9 - - - -
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Residues in contact with TYR 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ASP* 2.9 48.8 + - + +
45B GLN* 4.0 16.4 - - + +
46B LEU 3.4 0.4 - - - -
47B TYR* 1.3 97.2 - + - +
49B GLU* 1.3 60.5 + - + +
51B TYR* 3.1 7.0 + - - +
113B ALA* 3.7 47.3 - - + +
114B SER* 2.9 33.4 + - - -
139B PRO* 3.8 28.0 - - + +
141B GLU* 4.5 1.7 + - - -
351B ARG* 4.3 5.4 + - - -
401B SAH 3.9 30.4 + + - -
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Residues in contact with GLU 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B GLN* 2.7 49.2 + - - +
46B LEU* 3.5 25.1 - - - +
47B TYR 3.1 0.8 - - - -
48B TYR* 1.3 73.1 - - + +
50B CYS* 1.3 57.0 + - - +
51B TYR 2.8 9.7 + - - -
52B SER* 2.8 33.6 + - - +
53B ASP* 4.6 1.4 + - - +
114B SER* 4.8 0.2 - - - -
115B ALA* 6.1 0.4 - - + +
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Residues in contact with CYS 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU 3.4 11.8 + - - -
47B TYR* 2.9 23.3 + - + +
49B GLU* 1.3 76.2 - - - +
51B TYR* 1.3 66.3 + - + +
52B SER 3.6 0.2 - - - -
53B ASP* 5.1 3.7 + - - +
56B VAL* 4.1 19.4 - - - +
402B 49K 4.5 23.8 - - + -
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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
------------------------------------------------------------
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