Contacts of the helix formed by residues 29 - 45 (chain B) in PDB entry 1CPJ
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 CYS 29 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLN* 3.4 18.6 - - - +
27B GLY* 4.8 8.3 - - - -
28B SER* 1.3 77.8 - - - +
30B TRP* 1.3 64.4 + - - +
32B PHE* 4.0 6.4 - - - +
33B GLY 3.1 20.1 + - - -
198B GLY 5.1 2.2 - - - -
199B HIS* 3.1 44.2 - - + -
200B ALA* 3.4 29.3 - - - +
220B SER* 4.2 1.5 + - - +
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Residues in contact with TRP 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B GLY 3.3 17.1 + - - -
28B SER* 3.8 5.6 - - - +
29B CYS* 1.3 84.4 - - - +
31B ALA* 1.3 64.9 + - + +
34B ALA* 3.8 8.3 - - - +
59B LEU* 3.6 39.0 - - + -
60B LEU* 4.1 14.8 - - + -
63B CYS* 4.5 0.2 - - + -
67B CYS* 3.4 44.9 - - + -
70B GLY* 3.0 38.7 + - - -
73B GLY* 4.0 0.4 - - - -
74B GLY* 3.2 44.6 - - - +
75B TYR 4.4 4.3 - - - -
76B PRO* 3.9 12.2 - - + +
79B ALA* 4.0 11.2 - - + +
171B GLU* 3.0 17.8 - - - +
200B ALA* 3.5 13.9 - - + +
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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
----------------------------------------------------------
28B SER* 2.9 18.7 + - - +
30B TRP* 1.3 102.9 - - + +
32B PHE* 1.3 64.1 + - + +
33B GLY 3.4 0.2 - - - -
34B ALA 3.4 1.0 + - - -
35B VAL* 3.1 32.4 + - - +
56B ALA* 4.5 4.5 - - + +
59B LEU* 3.7 25.5 - - + +
60B LEU* 4.5 8.1 - - + -
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Residues in contact with PHE 32 (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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21B ARG* 3.2 49.8 - - + -
22B ASP 3.9 7.6 - - - -
23B GLN* 3.9 8.7 - - + -
28B SER* 3.0 29.5 + - - +
29B CYS 3.4 2.4 + - - +
31B ALA* 1.3 76.0 - - + +
33B GLY* 1.3 62.3 + - - +
35B VAL* 3.7 3.8 - - - +
36B GLU* 2.8 38.7 + - - +
56B ALA* 3.5 28.0 - - + -
60B LEU* 6.4 0.2 - - + -
103B TYR* 3.6 44.2 - + + -
220B SER* 3.8 26.9 - - - +
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Residues in contact with GLY 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B CYS 3.1 13.1 + - - -
32B PHE* 1.3 76.9 - - - +
34B ALA* 1.3 57.1 + - - +
36B GLU* 3.6 10.1 + - - -
37B ALA* 3.4 24.7 + - - +
171B GLU* 3.5 23.8 - - - +
200B ALA 5.0 0.2 + - - -
201B ILE* 3.9 18.8 - - - -
202B ARG* 3.9 5.9 - - - +
220B SER* 5.7 0.6 - - - -
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Residues in contact with ALA 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 TRP 3.8 7.4 - - - +
31B ALA 3.4 7.2 + - - +
32B PHE 3.2 0.8 - - - -
33B GLY* 1.3 76.4 - - - +
35B VAL* 1.3 62.8 + - - +
36B GLU 3.1 1.3 - - - -
37B ALA* 3.4 1.0 + - - -
38B MET* 2.8 46.8 + - + +
59B LEU* 4.1 2.7 - - + -
79B ALA* 3.9 11.4 - - + -
80B TRP* 3.5 15.6 - - - +
171B GLU* 3.1 23.7 + - - +
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Residues in contact with VAL 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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21B ARG* 3.6 23.1 - - - +
31B ALA 3.1 16.8 + - - +
32B PHE* 3.7 7.9 - - - +
34B ALA* 1.3 74.5 - - - +
36B GLU* 1.3 67.1 + - - +
38B MET* 3.5 7.7 - - - +
39B SER* 2.9 29.9 + - - -
54B VAL* 3.7 24.8 - - + +
55B SER 3.6 21.8 - - - +
56B ALA* 4.0 14.8 - - + +
59B LEU* 3.8 17.7 - - + -
88B LEU* 4.2 4.7 - - + -
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Residues in contact with GLU 36 (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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16B THR* 5.2 0.2 - - - -
19B GLN 5.1 0.8 - - - +
20B ILE* 5.6 0.2 - - - -
21B ARG* 2.9 52.6 + - + +
32B PHE* 2.8 38.0 + - - +
33B GLY* 3.6 8.7 - - - +
35B VAL* 1.3 79.1 - - - +
37B ALA* 1.3 60.6 + - - +
39B SER* 3.7 2.6 - - - -
40B ASP* 2.9 29.8 + - - +
202B ARG* 3.5 39.1 + - - +
218B ALA* 4.7 5.6 - - - +
219B ASN 4.7 2.8 - - - +
220B SER* 4.0 12.4 - - - -
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Residues in contact with ALA 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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33B GLY 3.4 17.3 + - - +
34B ALA 3.4 1.4 + - - -
36B GLU* 1.3 79.5 - - - +
38B MET* 1.3 57.5 + - - +
40B ASP* 3.5 7.4 - - - +
41B ARG* 3.0 31.7 + - - +
80B TRP* 3.8 22.7 - - + -
169B PRO 3.9 19.4 - - - +
170B VAL 4.2 11.4 - - - -
202B ARG* 3.8 10.0 - - - +
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Residues in contact with MET 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 ALA* 2.8 37.2 + - + +
35B VAL* 3.2 8.7 + - - +
37B ALA* 1.3 69.6 - - - +
39B SER* 1.3 58.9 + - - +
41B ARG* 3.1 6.4 + - - +
42B ILE* 2.8 35.9 + - - +
54B VAL* 4.2 8.5 - - + -
79B ALA* 4.1 3.4 - - + +
80B TRP* 3.4 49.8 - - + +
83B TRP* 3.6 49.9 - - + -
88B LEU* 3.6 26.7 - - + -
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Residues in contact with SER 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B THR* 3.5 20.4 - - - -
21B ARG* 4.1 5.7 + - - -
35B VAL 2.9 20.4 + - - -
36B GLU* 3.7 4.7 - - - -
38B MET* 1.3 69.1 - - - +
40B ASP* 1.3 68.1 + - - -
41B ARG 2.9 1.2 + - - -
42B ILE* 3.1 13.7 + - - +
43B CYS* 3.1 13.9 + - - +
52B VAL 3.4 20.0 + - - +
53B GLU* 3.9 1.7 - - - -
54B VAL* 3.0 31.5 + - - +
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Residues in contact with ASP 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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14B CYS* 4.8 0.2 - - - -
16B THR* 2.8 22.4 + - - +
17B ILE* 3.1 26.6 + - + +
36B GLU 2.9 15.8 + - - +
37B ALA* 3.5 10.1 - - - +
39B SER* 1.3 73.3 - - - +
41B ARG* 1.3 57.2 + - - +
43B CYS* 3.4 5.0 + - - +
44B ILE* 3.1 33.5 + - - +
169B PRO* 3.0 34.5 - - + +
202B ARG* 2.9 25.4 + - - -
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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
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37B ALA 3.0 17.9 + - - +
38B MET* 3.5 5.8 - - - +
39B SER 3.1 0.6 - - - -
40B ASP* 1.3 74.6 - - + +
42B ILE* 1.3 60.8 + - - +
44B ILE* 4.4 3.1 - - - +
45B HIS* 2.8 47.6 + - + +
80B TRP* 4.1 15.2 - - - -
83B TRP* 5.2 1.3 - - + -
151B TYR* 3.7 1.0 + - - -
163B GLU* 3.3 27.5 + - - +
167B ASN* 3.3 27.6 + - - +
168B GLY* 2.9 28.4 + - - -
169B PRO 3.1 17.1 + - - +
170B VAL* 3.8 10.7 - - - +
248B ALA* 4.0 5.5 - - - +
249B GLY 2.8 31.3 + - - +
250B ILE* 3.4 14.3 - - - +
251B PRO* 4.0 7.4 - - + -
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Residues in contact with ILE 42 (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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38B MET 2.8 25.0 + - - +
39B SER* 3.7 4.9 - - - +
41B ARG* 1.3 69.7 - - - +
43B CYS* 1.3 61.3 + - - +
45B HIS* 4.2 0.2 - - - +
46B THR* 2.9 30.7 + - - +
50B VAL* 3.5 35.4 - - + +
52B VAL* 4.1 13.7 - - + +
54B VAL* 3.6 26.5 - - + -
83B TRP* 4.2 13.5 - - + +
145B HIS* 4.4 19.7 - - + +
251B PRO* 3.9 23.1 - - + +
253B THR* 4.8 8.3 - - + -
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Residues in contact with CYS 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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13B ASN* 3.9 6.1 - - - -
14B CYS* 2.1 57.2 - - + -
16B THR* 5.1 2.2 - - - +
39B SER 3.1 10.3 + - - +
40B ASP* 3.5 9.0 - - - +
42B ILE* 1.3 76.3 - - - +
44B ILE* 1.3 59.7 + - - +
46B THR* 4.3 0.2 - - - -
47B ASN 3.5 0.7 + - - -
48B GLY* 2.9 34.8 + - - -
50B VAL 3.5 12.7 + - - +
51B ASN* 3.3 24.7 - - - +
52B VAL 6.0 0.7 - - - +
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Residues in contact with ILE 44 (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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11B TRP* 3.4 65.1 + - + +
14B CYS* 4.3 5.4 - - - -
17B ILE* 4.2 5.8 - - + -
40B ASP 3.1 25.3 + - - +
41B ARG* 4.0 4.0 - - - +
43B CYS* 1.3 75.4 - - - +
45B HIS* 1.3 79.9 + - + +
47B ASN* 3.3 16.9 + - - +
166B LYS 5.6 1.6 - - - +
167B ASN* 4.6 4.9 - - - +
168B GLY* 3.9 24.9 - - - -
169B PRO* 4.0 6.7 - - + -
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Residues in contact with HIS 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* 2.8 36.8 + - + +
42B ILE 4.2 0.2 - - - +
44B ILE* 1.3 83.9 - - + +
46B THR* 1.3 57.8 + - + +
47B ASN* 3.0 14.3 + - - +
166B LYS 5.0 2.5 - - - -
167B ASN* 3.1 48.9 + - - -
250B ILE* 4.2 17.8 - - + +
251B PRO* 3.5 30.7 - - + -
253B THR* 4.7 7.2 - - - +
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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