Contacts of the helix formed by residues 30 - 50 (chain D) in PDB entry 2YMB
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 ARG 30 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D LEU* 2.8 33.6 + - + +
28D GLU* 3.2 40.3 + - + +
29D SER* 1.3 74.7 - - - +
31D TYR* 1.3 58.0 + - - +
32D PRO* 3.5 4.9 - - - -
33D GLN* 3.3 22.7 + - - +
34D ALA* 2.8 27.9 + - - +
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Residues in contact with TYR 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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26D ASP* 3.5 21.2 + - - -
29D SER* 3.2 43.2 + - - -
30D ARG* 1.3 71.7 - - - +
32D PRO* 1.3 74.7 - - + +
34D ALA* 3.8 4.4 - - + +
35D LEU* 3.0 25.6 + - - +
71D ARG* 3.4 25.4 - - - -
75D ILE* 3.9 21.6 - - + +
79D LEU* 4.4 10.5 - - + -
88D TYR* 3.3 55.4 - + + -
89D HIS 3.9 2.5 - - - -
90D LYS* 3.3 4.3 - - - -
91D GLN* 3.0 31.2 + - - +
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Residues in contact with PRO 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29D SER 5.2 0.7 - - - +
30D ARG* 3.7 4.0 - - - -
31D TYR* 1.3 94.4 - - + +
33D GLN* 1.3 72.5 + - - +
35D LEU* 3.7 3.6 + - + +
36D VAL* 3.3 24.3 + - - +
79D LEU* 4.2 24.0 - - + -
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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
----------------------------------------------------------
25D LEU* 3.7 19.7 - - + -
30D ARG* 3.5 28.4 - - + +
32D PRO* 1.3 89.1 - - - +
34D ALA* 1.3 66.0 + - - +
35D LEU 3.2 0.2 - - - -
36D VAL* 3.3 8.2 + - - +
37D CYS* 3.2 25.5 + - - -
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Residues in contact with ALA 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22D ALA* 3.7 8.2 - - - +
25D LEU* 3.6 24.0 - - + +
26D ASP* 3.6 22.0 - - + +
30D ARG 2.8 19.7 + - - +
31D TYR* 3.8 6.3 - - - +
33D GLN* 1.3 75.8 - - - +
35D LEU* 1.3 58.2 + - - +
37D CYS* 3.4 3.8 + - - +
38D TYR* 3.0 38.3 + - + -
75D ILE* 4.9 2.7 - - + -
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Residues in contact with LEU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31D TYR 3.0 17.9 + - - +
32D PRO* 3.9 6.1 - - + +
33D GLN 3.2 0.2 - - - -
34D ALA* 1.3 77.0 - - - +
36D VAL* 1.3 63.0 + - + +
38D TYR* 3.1 9.7 + - - +
39D GLN* 3.0 46.1 + - + +
72D ALA* 3.3 40.2 - - + +
75D ILE* 4.3 7.6 - - + +
76D LYS* 4.1 31.6 - - + +
79D LEU* 4.4 12.6 - - + -
194H LEU* 4.4 7.2 - - + +
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Residues in contact with VAL 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 PRO 3.3 17.5 - - - +
33D GLN* 3.3 9.3 + - - +
35D LEU* 1.3 76.8 - - + +
37D CYS* 1.3 64.3 + - - +
39D GLN* 3.3 19.6 + - + +
40D GLU* 3.1 29.5 + - + +
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Residues in contact with CYS 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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18D VAL* 3.3 21.7 - - + +
21D ARG* 4.3 20.9 - - - -
22D ALA* 3.5 24.3 - - + +
25D LEU* 3.9 17.7 - - - -
33D GLN* 3.2 14.9 + - - +
34D ALA 3.7 4.0 - - - +
35D LEU 3.3 0.2 - - - -
36D VAL* 1.3 77.1 - - - +
38D TYR* 1.3 61.5 + - - +
40D GLU* 3.4 2.2 + - - -
41D GLY* 2.8 26.0 + - - -
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Residues in contact with TYR 38 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 4.2 12.6 - - + +
22D ALA* 3.5 28.5 + - + -
23D VAL* 3.8 13.0 - - + +
26D ASP* 2.8 37.1 + - + +
34D ALA 3.0 25.3 + - - -
35D LEU* 3.1 9.2 + - - +
37D CYS* 1.3 77.6 - - - +
39D GLN* 1.3 52.6 + - - +
41D GLY 3.3 0.5 + - - -
42D ILE* 2.8 42.6 + - + +
68D TYR* 3.9 31.2 - + + -
71D ARG* 3.9 13.5 - - + +
72D ALA* 3.9 22.9 - - + -
75D ILE* 3.7 19.5 - - + -
93D LYS* 5.5 3.3 + - - -
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Residues in contact with GLN 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 LEU* 3.0 31.4 + - + +
36D VAL* 3.4 35.1 - - + +
38D TYR* 1.3 77.6 - - - +
40D GLU* 1.3 55.9 + - + +
42D ILE* 3.6 1.3 + - - -
43D ASP* 2.9 29.5 + - - +
191H LEU* 3.6 11.3 - - + +
194H LEU* 3.2 41.1 + - + +
195H ARG* 3.2 43.7 + - - +
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Residues in contact with GLU 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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18D VAL* 4.2 13.0 - - + -
36D VAL* 3.1 24.8 + - + +
37D CYS* 3.9 4.9 - - - +
39D GLN* 1.3 74.5 - - + +
41D GLY* 1.3 60.8 + - - +
43D ASP* 3.8 8.6 - - - +
44D LEU* 3.0 42.6 + - + +
195H ARG* 3.0 26.4 + - - -
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Residues in contact with GLY 41 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D ALA* 4.5 3.1 - - - +
18D VAL* 3.7 11.6 - - - +
19D LEU* 3.7 28.2 - - - +
37D CYS 2.8 17.4 + - - -
40D GLU* 1.3 76.3 - - - +
42D ILE* 1.3 62.9 + - - +
44D LEU* 3.6 4.8 + - - +
45D LEU* 3.3 26.2 + - - +
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Residues in contact with ILE 42 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D LEU* 5.0 1.1 - - + -
38D TYR* 2.8 26.0 + - + +
39D GLN 3.8 3.8 - - - +
41D GLY* 1.3 72.7 - - - +
43D ASP* 1.3 65.4 + - - +
45D LEU* 3.0 20.4 + - - +
46D LEU* 3.1 15.6 + - + +
65D ILE* 4.3 10.7 - - + +
68D TYR* 4.0 22.7 - - + +
69D MET* 3.6 63.0 - - + +
72D ALA* 4.2 12.3 - - + -
191H LEU* 3.9 16.2 - - + -
194H LEU* 4.4 4.5 - - + -
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Residues in contact with ASP 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 GLN 2.9 19.0 + - - +
40D GLU* 3.8 13.8 - - - +
41D GLY 3.4 0.2 - - - -
42D ILE* 1.3 76.3 - - - +
44D LEU* 1.3 62.7 + - + +
46D LEU* 3.3 8.9 + - - +
47D GLN* 3.3 40.0 + - - +
191H LEU* 3.6 19.5 - - + +
195H ARG* 3.3 26.7 + - - +
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Residues in contact with LEU 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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11D GLN* 3.7 16.6 + - - +
14D ALA* 4.2 11.7 - - + +
15D ALA* 3.6 36.6 - - + +
18D VAL* 4.3 13.2 - - + -
40D GLU* 3.0 30.8 + - + +
41D GLY 3.8 1.3 - - - +
43D ASP* 1.3 78.4 - - + +
45D LEU* 1.3 62.8 + - - +
47D GLN* 3.4 25.0 + - - +
48D VAL* 3.2 26.5 + - - +
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Residues in contact with LEU 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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12D SER* 5.4 3.6 - - - +
15D ALA* 3.9 19.7 - - + -
19D LEU* 3.8 23.1 - - + -
41D GLY 3.3 12.3 + - - +
42D ILE* 3.0 12.9 + - - +
44D LEU* 1.3 75.5 - - - +
46D LEU* 1.3 55.7 + - - +
48D VAL* 3.2 11.4 + - + +
49D LEU* 2.7 35.5 + - - +
61D LEU* 4.2 11.1 - - + +
64D LYS* 4.3 30.7 - - + +
65D ILE* 3.7 30.8 - - + +
68D TYR* 4.5 7.0 - - + -
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Residues in contact with LEU 46 (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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42D ILE* 3.1 17.9 + - + +
43D ASP* 3.5 9.9 - - - +
44D LEU 3.3 0.4 - - - -
45D LEU* 1.3 73.8 - - - +
47D GLN* 1.3 57.4 + - + +
48D VAL 3.0 5.2 - - - -
49D LEU* 4.1 10.8 - - + -
50D LYS* 2.9 54.8 + - - +
65D ILE* 3.7 22.9 - - + -
184H GLU* 5.5 1.3 - - - -
187H LEU* 4.0 21.8 - - + +
188H SER* 3.8 31.2 - - - +
191H LEU* 3.8 28.9 - - + -
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Residues in contact with GLN 47 (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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11D GLN* 4.1 13.9 + - - +
43D ASP* 3.3 34.1 + - - +
44D LEU* 3.5 29.2 - - - +
45D LEU 3.3 0.6 - - - -
46D LEU* 1.3 76.9 - - + +
48D VAL* 1.3 59.5 + - - +
50D LYS* 4.4 5.9 - - - +
51D GLY* 4.1 10.0 + - - -
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Residues in contact with VAL 48 (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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11D GLN* 3.2 21.8 - - - +
12D SER* 3.7 29.8 - - - -
15D ALA* 5.5 0.2 - - + -
44D LEU 3.2 16.8 - - - +
45D LEU* 3.2 14.1 + - + +
46D LEU 3.0 0.4 - - - -
47D GLN* 1.3 79.1 - - - +
49D LEU* 1.3 60.0 + - - +
50D LYS 3.3 0.4 - - - -
51D GLY* 3.0 2.8 + - - -
52D THR* 2.8 39.4 + - + +
61D LEU* 3.8 17.0 - - + -
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Residues in contact with LEU 49 (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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45D LEU 2.7 21.3 + - - +
46D LEU* 3.3 12.5 + - + +
48D VAL* 1.3 75.2 - - - +
50D LYS* 1.3 57.6 + - + +
51D GLY 3.0 2.3 + - - -
52D THR* 3.1 19.2 + - - +
58D ARG* 3.4 44.1 - - + +
61D LEU* 3.7 24.7 - - + -
62D ARG 4.7 0.7 - - - +
65D ILE* 3.8 19.7 - - + -
183H MET* 3.9 10.1 - - + -
184H GLU* 3.2 33.8 - - + +
187H LEU* 3.9 18.4 - - + -
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Residues in contact with LYS 50 (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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46D LEU* 2.9 36.8 + - - +
47D GLN* 4.8 5.4 - - + -
49D LEU* 1.3 76.5 - - + +
51D GLY* 1.3 57.3 + - - +
52D THR 4.8 1.1 - - - -
184H GLU* 3.3 50.8 - - + +
188H SER* 3.9 20.8 + - - -
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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