Contacts of the helix formed by residues 12 - 34 (chain B) in PDB entry 3C2B
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 12 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B PHE* 1.3 77.3 - - - +
13B PRO* 1.4 64.9 - - - +
14B ARG* 3.2 14.8 + - - +
15B GLN* 2.8 37.5 + - - +
16B ASN* 2.8 33.1 + - - +
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Residues in contact with PRO 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE 4.5 0.7 - - - +
12B SER* 1.4 87.6 - - - +
14B ARG* 1.3 54.6 + - - +
16B ASN* 3.4 11.8 - - + +
17B ALA* 3.0 23.9 + - - +
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Residues in contact with ARG 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B SER* 3.2 15.0 + - - +
13B PRO* 1.3 75.9 - - - +
15B GLN* 1.3 69.1 + - + +
16B ASN 3.1 1.1 - - - -
17B ALA* 3.2 16.7 + - + +
18B VAL* 3.2 20.6 + - - +
44B ASN 5.7 3.0 + - - -
45B CYS* 4.9 8.3 - - - +
49B SER* 5.7 0.8 + - - -
53B TRP* 3.8 35.7 - - + -
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Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.6 30.9 - - + -
12B SER* 2.8 40.6 + - - +
14B ARG* 1.3 72.8 - - + +
16B ASN* 1.3 62.1 + - - +
18B VAL* 3.3 10.8 + - - +
19B LEU* 3.1 27.7 + - - +
53B TRP* 3.3 63.0 + - + +
54B PHE* 4.3 6.3 - - + -
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Residues in contact with ASN 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.5 27.8 + - - +
12B SER 2.8 23.0 + - - +
13B PRO* 3.4 11.9 - - + +
15B GLN* 1.3 74.0 - - - +
17B ALA* 1.3 58.2 + - - +
19B LEU* 3.4 1.9 + - - +
20B ASP* 3.0 28.3 + - - +
67B PHE* 3.3 37.9 - - + -
70B SER* 5.3 3.2 + - - -
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Residues in contact with ALA 17 (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 PRO 3.0 14.8 + - - +
14B ARG* 3.2 13.4 + - - +
16B ASN* 1.3 74.1 - - - +
18B VAL* 1.3 59.2 + - + +
20B ASP* 3.4 9.6 + - - +
21B GLN* 3.1 31.8 + - + +
43B ALA* 5.7 0.2 - - - -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG* 3.2 15.0 + - + +
15B GLN* 3.4 9.0 - - - +
17B ALA* 1.3 74.1 - - + +
19B LEU* 1.3 66.4 + - - +
20B ASP 3.1 1.3 - - - -
21B GLN* 3.1 11.1 + - - +
22B ALA* 2.9 21.0 + - - +
39B LEU* 3.7 11.9 - - + +
43B ALA* 4.0 22.0 - - + +
45B CYS* 4.0 17.5 - - + -
50B LEU* 3.6 28.9 - - + -
53B TRP* 4.0 8.3 - - + -
54B PHE* 4.0 11.4 - - + -
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Residues in contact with LEU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B PHE* 3.7 41.5 - - + -
15B GLN 3.1 15.3 + - - +
16B ASN* 3.4 3.3 + - - +
18B VAL* 1.3 76.3 - - - +
20B ASP* 1.3 58.1 + - - +
22B ALA* 3.2 4.8 + - - +
23B LEU* 2.9 31.7 + - - +
54B PHE* 3.8 23.1 - - + -
60B LEU* 3.9 16.8 - - + -
63B ALA* 3.8 18.2 - - + +
64B MSE 3.9 14.0 - - + +
67B PHE* 3.8 33.0 - - + -
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Residues in contact with ASP 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ASN 3.0 14.4 + - - +
17B ALA* 3.4 13.3 - - - +
18B VAL 3.1 0.2 - - - -
19B LEU* 1.3 78.1 - - - +
21B GLN* 1.3 56.9 + - - +
23B LEU* 3.4 5.6 + - - +
24B ARG* 3.0 46.8 + - - +
67B PHE* 3.7 22.4 - - + -
71B LYS* 4.5 10.7 + - - -
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Residues in contact with GLN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ALA* 3.1 20.8 + - + +
18B VAL 3.3 7.6 - - - +
20B ASP* 1.3 75.4 - - - +
22B ALA* 1.3 59.4 + - - +
24B ARG* 3.3 23.2 + - - +
25B LEU* 2.8 33.0 + - - +
39B LEU* 3.9 12.6 - - + -
42B ALA* 3.3 31.2 + - + +
43B ALA* 4.0 18.0 - - + +
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B VAL 2.9 13.0 + - - +
19B LEU* 3.2 10.3 + - - +
21B GLN* 1.3 77.0 - - - +
23B LEU* 1.3 61.7 + - - +
25B LEU* 3.3 6.7 + - - +
26B LEU 3.2 15.8 + - - -
34B LEU* 3.5 17.8 - - + +
39B LEU* 3.5 27.7 - - + +
60B LEU* 4.5 1.1 - - + -
64B MSE 3.7 29.3 - - + +
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Residues in contact with LEU 23 (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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19B LEU 2.9 12.2 + - - +
20B ASP* 3.7 7.9 - - - +
22B ALA* 1.3 75.7 - - - +
24B ARG* 1.3 59.1 + - - +
26B LEU* 3.1 5.9 + - + +
27B VAL* 2.9 33.1 + - - +
64B MSE 3.5 35.0 - - + +
67B PHE* 3.5 32.5 - - + -
68B GLN* 3.3 28.3 - - + +
71B LYS* 4.4 3.8 - - - +
106B VAL* 3.9 27.1 - - + -
110B LEU* 4.2 15.3 - - + -
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Residues in contact with ARG 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ASP* 3.0 35.3 + - - +
21B GLN* 3.7 20.5 + - - +
23B LEU* 1.3 73.6 - - - +
25B LEU* 1.3 63.1 + - + +
27B VAL* 4.5 6.3 - - - -
28B GLU* 2.9 68.6 + - - +
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B GLN 2.8 16.6 + - - +
22B ALA* 3.4 9.9 - - - +
23B LEU 3.3 0.2 - - - -
24B ARG* 1.3 78.0 - - + +
26B LEU* 1.3 56.0 + - - +
28B GLU* 4.9 2.0 - - - -
29B GLY* 2.7 34.6 + - - +
30B GLY 3.5 0.9 + - - -
33B ALA* 3.7 42.7 - - + +
34B LEU* 4.6 7.2 - - + -
38B GLY* 3.9 7.6 - - - +
39B LEU* 3.8 36.1 - - + +
42B ALA* 4.3 16.4 - - + -
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Residues in contact with LEU 26 (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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22B ALA 3.2 9.1 + - - +
23B LEU* 3.1 10.0 + - + +
25B LEU* 1.3 76.9 - - - +
27B VAL* 1.3 66.6 + - + +
30B GLY* 3.0 42.0 + - - -
31B GLU* 3.9 1.1 - - - +
34B LEU* 4.0 20.2 - - + -
64B MSE 4.5 6.7 - - + -
109B ALA* 4.2 23.6 - - + +
110B LEU* 3.7 34.1 - - + -
113B LEU* 3.8 30.3 - - + -
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A ARG* 5.9 0.7 + - - -
23B LEU 2.9 19.9 + - - +
24B ARG* 3.9 6.3 - - - +
26B LEU* 1.3 77.4 - - + +
28B GLU* 1.3 71.0 + - + +
30B GLY 4.6 0.7 + - - -
105B ASP* 3.9 29.8 - - + +
106B VAL* 3.9 39.3 - - + +
109B ALA* 4.0 12.9 - - + +
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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
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120A ARG* 5.4 8.1 + - - +
24B ARG* 2.9 56.7 + - - +
25B LEU* 4.2 2.3 - - - +
27B VAL* 1.3 84.8 - - + +
29B GLY* 1.3 58.0 + - - +
30B GLY 3.6 0.6 + - - -
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Residues in contact with GLY 29 (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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25B LEU* 2.7 17.1 + - - +
28B GLU* 1.3 75.1 - - - +
30B GLY* 1.3 65.6 + - - +
32B LYS* 4.1 7.3 + - - +
33B ALA* 3.5 20.8 + - - +
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Residues in contact with GLY 30 (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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25B LEU 3.9 3.3 - - - +
26B LEU* 3.0 31.6 + - - +
27B VAL 4.6 0.6 + - - -
28B GLU 3.6 1.6 + - - -
29B GLY* 1.3 82.8 - - - +
31B GLU* 1.3 63.2 + - - -
32B LYS 3.3 0.2 - - - -
33B ALA* 3.3 7.1 + - - +
34B LEU* 3.4 8.3 + - - +
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Residues in contact with GLU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B LEU* 3.9 8.7 - - - +
30B GLY* 1.3 68.7 - - - -
32B LYS* 1.3 67.1 + - - +
34B LEU* 3.2 23.3 + - - +
35B THR* 4.8 1.2 - - - +
57B ARG* 4.1 19.2 + - - +
113B LEU* 3.6 32.8 - - + +
117B GLN* 3.5 19.2 + - - +
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Residues in contact with LYS 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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29B GLY 4.3 7.2 - - - +
30B GLY 3.3 0.4 - - - -
31B GLU* 1.3 77.0 - - - +
33B ALA* 1.3 60.2 + - - +
35B THR* 3.4 19.6 - - - +
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Residues in contact with ALA 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.7 39.8 - - + +
29B GLY* 3.5 26.9 + - - +
30B GLY 3.3 4.8 + - - +
31B GLU 3.2 0.4 - - - -
32B LYS* 1.3 77.5 - - - +
34B LEU* 1.3 58.4 + - - +
35B THR* 2.9 13.6 + - - +
38B GLY* 4.3 5.2 - - - -
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Residues in contact with LEU 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA* 3.5 33.4 - - + +
25B LEU* 4.6 7.8 - - + +
26B LEU* 4.0 25.1 - - + -
30B GLY 3.4 9.1 + - - +
31B GLU* 3.2 16.1 + - - +
33B ALA* 1.3 74.8 - - - +
35B THR* 1.3 56.9 - - - +
39B LEU* 5.6 1.6 - - + -
57B ARG* 2.2 48.1 + - - +
60B LEU* 4.7 9.9 - - + -
61B LEU* 3.6 29.8 - - + -
64B MSE 4.0 16.4 - - + -
113B LEU* 4.8 6.3 - - + -
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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
------------------------------------------------------------
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