Contacts of the helix formed by residues 30 - 48 (chain D) in PDB entry 6CAJ
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 30 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28D PRO* 3.9 4.0 - - - +
29D ARG* 1.3 80.5 - - - +
31D SER* 1.3 60.8 + - - +
32D GLU* 3.3 16.0 + - - +
33D GLU* 3.7 26.3 + - - +
34D MET* 3.1 25.2 + - - +
148D MET* 5.4 2.9 - - - +
172D ARG* 3.5 35.5 + - - +
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Residues in contact with SER 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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29D ARG 3.7 2.6 + - - -
30D SER* 1.3 71.7 + - - +
32D GLU* 1.3 59.9 + - - +
34D MET* 3.4 8.2 + - - +
35D ALA* 2.9 27.4 + - - +
75D GLU* 4.4 4.7 + - - -
77D THR* 3.6 20.8 + - - +
172D ARG* 5.0 0.2 - - - +
237D LYS* 5.1 9.4 + - - -
272D PHE* 3.2 20.9 - - - -
273D LYS* 3.9 18.9 - - - -
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Residues in contact with GLU 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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30D SER* 3.3 9.6 + - - +
31D SER* 1.3 75.7 - - - +
33D GLU* 1.3 58.2 + - - +
35D ALA* 3.3 3.0 + - - +
36D ARG* 2.9 39.0 + - - +
144D LEU* 3.3 36.0 - - + +
145D GLU* 4.0 14.6 - - - +
147D THR* 5.4 1.5 + - - -
148D MET* 3.4 40.4 + - + +
272D PHE* 3.9 19.1 - - + -
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Residues in contact with GLU 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28D PRO* 3.6 26.9 - - + +
29D ARG* 4.7 1.0 + - - +
30D SER* 3.5 25.3 + - - +
31D SER 3.3 0.6 - - - -
32D GLU* 1.3 78.3 - - - +
34D MET* 1.3 57.2 + - - +
36D ARG* 3.3 32.8 + - - +
37D GLU* 2.9 40.8 + - + +
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Residues in contact with MET 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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18D PHE* 4.5 8.2 - - + -
22D LEU* 4.7 8.7 - - + -
26D GLY* 4.8 3.4 - - - -
27D GLY 3.4 28.7 - - - +
28D PRO* 3.5 31.6 - - + +
30D SER 3.1 12.5 + - - +
31D SER* 3.7 10.8 - - - +
32D GLU 3.3 0.2 - - - -
33D GLU* 1.3 74.4 - - - +
35D ALA* 1.3 53.1 + - - +
37D GLU* 3.4 4.1 + - - +
38D THR* 2.5 36.8 + - - -
75D GLU* 3.3 43.3 - - + +
77D THR* 3.9 4.9 - - - +
78D VAL* 4.2 16.4 - - + -
237D LYS* 6.1 0.2 - - - +
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Residues in contact with ALA 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 SER 2.9 17.2 + - - +
32D GLU* 3.3 6.9 + - - +
34D MET* 1.3 74.4 - - - +
36D ARG* 1.3 59.6 + - - +
38D THR* 3.1 7.8 + - - -
39D LEU* 2.9 36.3 + - - +
77D THR* 5.7 5.3 + - - +
81D MET* 4.6 8.1 - - + -
144D LEU* 3.9 23.1 - - + -
272D PHE* 4.0 20.2 - - + -
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Residues in contact with ARG 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 GLU* 2.9 29.1 + - - +
33D GLU* 3.3 37.1 + - - +
35D ALA* 1.3 76.2 - - - +
37D GLU* 1.3 58.1 + - + +
39D LEU* 3.4 2.6 + - - +
40D GLY* 2.9 24.6 + - - -
141D LEU* 4.0 24.4 - - + +
144D LEU* 3.8 18.2 - - + -
145D GLU* 4.8 17.0 - - - -
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Residues in contact with GLU 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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14D ARG* 4.2 19.0 + - - +
18D PHE* 4.0 22.3 - - + -
28D PRO* 3.3 31.6 - - - +
33D GLU* 2.9 33.2 + - + +
34D MET 3.8 4.5 - - - +
36D ARG* 1.3 75.0 - - + +
38D THR* 1.3 59.9 + - - +
40D GLY* 3.7 1.6 - - - +
41D LEU* 2.9 29.3 + - - +
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Residues in contact with THR 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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18D PHE* 4.1 7.2 - - + -
34D MET 2.5 21.8 + - - -
35D ALA* 3.1 12.3 + - - -
37D GLU* 1.3 74.1 - - - +
39D LEU* 1.3 60.1 + - - +
41D LEU* 3.3 7.5 + - + +
42D LEU* 2.9 38.4 + - + +
68D MET* 5.7 3.1 - - + -
77D THR 5.4 0.3 - - - -
78D VAL* 3.3 36.7 - - + +
81D MET* 3.9 28.5 - - + -
82D VAL* 4.6 3.6 - - + -
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Residues in contact with LEU 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 ALA 2.9 27.4 + - - +
36D ARG 3.9 3.8 - - - +
38D THR* 1.3 76.1 - - - +
40D GLY* 1.3 59.0 + - - +
42D LEU* 3.4 7.1 + - - +
43D ARG* 2.9 34.1 + - - +
81D MET* 3.6 37.5 - - + -
85D VAL* 5.2 3.6 - - + -
137D ILE* 3.5 36.7 - - + +
140D LEU* 3.7 21.5 - - + -
141D LEU* 3.7 31.0 - - + +
144D LEU* 4.2 8.3 - - + -
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Residues in contact with GLY 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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14D ARG* 4.1 9.6 - - - -
36D ARG 2.9 15.6 + - - -
37D GLU* 3.7 4.0 - - - -
38D THR 3.2 0.2 - - - -
39D LEU* 1.3 76.9 - - - +
41D LEU* 1.3 55.5 + - - +
43D ARG* 3.3 14.5 - - - +
44D GLN* 2.9 31.9 + - - +
141D LEU* 6.0 1.3 - - - +
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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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11D LEU* 6.1 2.2 - - + -
14D ARG* 3.4 27.9 - - + +
15D ILE* 3.8 33.4 - - + +
18D PHE* 3.8 35.7 - - + -
37D GLU 2.9 18.7 + - - +
38D THR* 3.3 7.4 + - + +
40D GLY* 1.3 75.0 - - - +
42D LEU* 1.3 60.8 + - + +
44D GLN* 3.8 3.5 - - + +
45D ILE* 2.9 30.4 + - + +
64D GLU* 3.6 25.8 - - - +
68D MET* 3.8 9.4 - - + -
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Residues in contact with LEU 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 THR* 2.9 29.1 + - + +
39D LEU* 3.9 5.6 - - - +
40D GLY 3.3 0.2 - - - -
41D LEU* 1.3 78.0 - - + +
43D ARG* 1.3 60.0 + - - +
45D ILE* 3.2 6.9 - - + +
46D ILE* 3.0 32.0 + - + +
61D ILE* 4.0 30.1 - - + -
64D GLU* 4.2 12.6 - - - +
68D MET* 5.4 1.3 - - + -
81D MET* 4.4 1.8 - - + +
82D VAL* 3.9 34.8 - - + -
85D VAL* 3.7 41.1 - - + -
137D ILE* 5.0 5.6 - - + -
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Residues in contact with ARG 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 LEU 2.9 20.0 + - - +
40D GLY* 3.3 16.4 - - - +
42D LEU* 1.3 76.3 - - - +
44D GLN* 1.3 51.5 + - + +
46D ILE* 3.4 10.5 - - + +
47D THR* 2.7 41.4 + - + +
134D ILE* 4.8 15.0 - - + +
137D ILE* 3.2 51.1 + - + +
138D ASN* 2.6 32.4 + - - +
141D LEU* 3.3 27.3 - - - +
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Residues in contact with GLN 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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10D GLU* 4.7 16.0 + - - +
11D LEU* 3.4 32.6 - - + +
14D ARG* 3.2 42.7 + - - +
40D GLY 2.9 17.0 + - - +
41D LEU* 3.8 5.8 - - + +
42D LEU 3.3 0.2 - - - -
43D ARG* 1.3 78.9 - - + +
45D ILE* 1.3 60.8 + - - +
47D THR* 3.3 14.2 + - - +
48D ASP* 3.5 19.1 + - - +
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Residues in contact with ILE 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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11D LEU* 4.1 4.0 - - + +
15D ILE* 3.8 20.2 - - + -
41D LEU* 2.9 19.8 + - + +
42D LEU* 3.2 22.7 - - + +
44D GLN* 1.3 77.0 - - - +
46D ILE* 1.3 59.1 + - + +
49D HIS* 2.6 50.2 + - + +
60D LEU* 4.1 21.3 - - + +
61D ILE* 3.8 21.8 - - + -
64D GLU* 3.7 32.8 - - + +
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Residues in contact with ILE 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 LEU* 3.0 22.2 + - + +
43D ARG* 3.4 11.0 - - - +
45D ILE* 1.3 85.8 - - + +
47D THR* 1.3 66.0 + - + +
48D ASP 3.4 0.6 + - - -
49D HIS 4.1 0.3 + - - -
51D TRP* 3.2 31.4 - - + -
57D LEU* 4.2 31.9 - - + -
60D LEU* 6.5 0.4 - - + -
61D ILE* 4.5 7.2 - - + -
85D VAL* 6.2 1.1 - - + -
89D ILE* 5.1 3.4 - - + -
130D GLN* 3.7 12.9 + - + -
133D ILE* 3.9 29.8 - - + -
134D ILE* 3.7 32.5 - - + -
137D ILE* 4.9 2.7 - - + -
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Residues in contact with THR 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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43D ARG* 2.7 26.1 + - + +
44D GLN* 3.3 14.0 + - - +
46D ILE* 1.3 80.9 - - + +
48D ASP* 1.3 68.5 + - - +
49D HIS 3.6 2.5 + - - +
130D GLN* 3.9 17.2 + - - +
134D ILE* 3.7 28.0 - - + -
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Residues in contact with ASP 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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8D GLY 5.1 4.5 + - - +
11D LEU* 3.5 32.8 - - + +
44D GLN* 3.5 16.8 + - - +
46D ILE 3.4 0.8 - - - -
47D THR* 1.3 95.5 + - - +
49D HIS* 1.3 71.7 + - - +
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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