Contacts of the helix formed by residues 17 - 35 (chain B) in PDB entry 2CHT
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 GLU 17 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B THR* 1.3 70.6 - - - +
18B GLU* 1.3 62.7 + - - +
20B ILE* 3.8 0.3 - - - +
21B LEU* 3.0 38.1 + - + +
55B ALA* 3.4 15.2 - - + +
56B VAL* 3.5 36.0 - - + +
60B LYS* 2.9 29.7 + - - -
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ARG* 5.1 5.5 + - - +
16B THR* 3.2 11.7 + - + +
17B GLU* 1.3 78.7 + - - +
19B GLU* 1.3 54.7 + - - +
21B LEU* 3.7 4.4 - - - +
22B GLN* 2.8 51.4 + - + +
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 3.7 8.4 - - + -
13B GLU* 3.1 22.1 + - - +
14B ARG* 2.9 69.3 + - - +
16B THR* 3.1 9.1 + - + +
18B GLU* 1.3 77.4 + - - +
20B ILE* 1.3 60.6 + - - +
22B GLN* 4.0 18.2 - - - +
23B LYS* 2.8 59.3 + - + +
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Residues in contact with ILE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B VAL* 3.9 20.6 - - + -
14B ARG 4.6 2.0 - - - +
15B ASP* 3.3 26.2 - - - +
16B THR 3.0 19.0 + - - +
17B GLU 3.8 2.9 - - - +
19B GLU* 1.3 76.4 - - - +
21B LEU* 1.3 59.5 + - + +
24B THR* 2.7 37.4 + - - -
53B LEU* 4.4 14.6 - - + -
55B ALA* 3.9 12.6 - - + +
56B VAL* 3.6 30.3 - - + +
58B PRO* 4.1 15.0 - - + -
89B ILE* 3.9 18.8 - - + +
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Residues in contact with LEU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B GLU* 3.0 35.3 + - + +
18B GLU* 3.8 3.4 - - - +
20B ILE* 1.3 78.8 - - + +
22B GLN* 1.3 63.3 + - - +
25B LYS* 2.9 29.0 + - - +
56B VAL* 3.5 21.8 - - + -
57B PHE 4.2 2.7 - - - +
58B PRO 4.4 1.8 - - - +
60B LYS* 3.9 36.3 - - + +
61B ALA* 3.7 15.8 - - + +
64B GLU* 3.9 24.5 - - - +
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Residues in contact with GLN 22 (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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18B GLU* 2.8 34.7 + - + +
19B GLU* 4.0 18.9 - - - +
21B LEU* 1.3 71.2 - - - +
23B LYS* 1.3 76.9 + - - +
25B LYS* 3.5 14.9 + - - +
26B GLN* 3.0 57.0 + - + +
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Residues in contact with LYS 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 3.4 25.1 + - + +
11B THR 4.0 7.4 + - - +
12B VAL* 4.0 14.4 - - + -
19B GLU* 2.8 47.1 + - + +
22B GLN* 1.3 93.6 + - - +
24B THR* 1.3 61.3 + - - +
26B GLN* 3.7 23.6 + - - +
27B LEU* 3.3 14.7 + - - +
89B ILE* 5.8 0.4 - - + -
109B LEU* 5.8 0.2 - - - +
110B GLU* 3.5 41.1 + - + +
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Residues in contact with THR 24 (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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10B THR* 4.5 3.4 - - - -
20B ILE 2.7 27.6 + - - -
23B LYS* 1.3 70.0 - - - +
25B LYS* 1.3 54.4 + - - +
27B LEU* 2.9 11.2 + - + +
28B LEU* 2.8 42.7 + - + +
47B LEU* 3.8 26.7 - - + -
58B PRO* 3.7 17.2 - - - +
61B ALA* 3.6 21.3 - - + -
89B ILE* 3.7 21.6 - - + +
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Residues in contact with LYS 25 (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 LEU 2.9 15.5 + - - +
22B GLN* 3.7 18.7 - - - +
24B THR* 1.3 74.8 - - - +
26B GLN* 1.3 58.8 + - - +
28B LEU* 3.2 9.6 + - - +
29B GLU* 2.8 50.7 + - - +
61B ALA* 3.7 13.8 - - + +
64B GLU* 3.7 40.2 + - + +
65B LEU* 3.9 13.4 - - + +
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B THR* 5.9 0.2 + - - -
22B GLN* 3.0 44.5 + - + +
23B LYS* 3.7 30.8 + - - +
25B LYS* 1.3 76.5 - - - +
27B LEU* 1.3 67.3 + - - +
29B GLU* 3.9 16.8 - - - +
30B LYS* 3.3 19.2 + - - +
109B LEU* 3.9 13.4 - - + +
110B GLU* 4.2 7.7 + - - +
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Residues in contact with LEU 27 (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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8B GLY* 3.9 3.6 - - - -
9B ALA* 3.6 36.8 - - - +
10B THR* 3.7 22.9 - - + +
23B LYS 3.3 10.3 + - - +
24B THR* 2.9 12.0 + - + +
26B GLN* 1.3 76.1 - - - +
28B LEU* 1.3 67.5 + - + +
30B LYS* 2.8 14.6 + - - +
31B ILE* 3.0 16.5 + - + +
47B LEU* 5.3 2.9 - - + -
89B ILE* 4.4 8.3 - - + +
90B ARG 5.2 0.4 - - - -
91B VAL* 3.6 29.6 - - + +
107B VAL* 3.7 26.7 - - + +
109B LEU* 4.0 9.8 - - + +
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B THR* 2.8 34.0 + - + +
25B LYS* 3.4 7.9 - - - +
27B LEU* 1.3 77.5 - - + +
29B GLU* 1.3 62.9 + - - +
30B LYS 3.1 0.3 + - - -
31B ILE* 3.1 7.9 + - + +
32B ILE* 3.1 33.7 + - + +
45B MET* 3.5 31.4 - - + -
47B LEU* 5.3 1.3 - - + -
61B ALA 4.3 3.8 - - - +
62B VAL* 3.7 32.5 - - + +
65B LEU* 3.9 24.0 - - + -
68B TRP* 5.6 0.4 - - + -
91B VAL* 4.5 16.4 - - + -
93B MET* 5.6 4.3 - - - -
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Residues in contact with GLU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LYS* 2.8 47.5 + - + +
26B GLN* 4.0 16.2 - - - +
28B LEU* 1.3 71.4 - - - +
30B LYS* 1.3 62.7 + - - +
32B ILE* 3.6 9.0 + - + +
33B GLU* 3.0 26.3 + - - +
65B LEU* 4.5 11.4 - - + +
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Residues in contact with LYS 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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26B GLN 3.3 11.8 + - - +
27B LEU 2.8 10.3 + - - +
29B GLU* 1.3 79.9 - - - +
31B ILE* 1.3 58.8 + - - +
33B GLU* 2.9 27.4 + - - +
34B GLU* 2.9 54.4 + - - +
107B VAL* 3.5 28.3 - - + -
109B LEU* 4.3 15.5 - - + -
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Residues in contact with ILE 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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6B ILE* 3.6 19.5 - - + +
7B ARG 4.2 3.4 - - - +
8B GLY* 3.9 15.5 - - - +
27B LEU* 3.0 16.7 + - + +
28B LEU* 3.6 11.9 - - + +
30B LYS* 1.3 75.1 - - - +
32B ILE* 1.3 51.9 + - + +
35B ASN* 2.7 44.0 + - - +
91B VAL* 3.6 34.8 - - + -
93B MET* 3.3 32.1 - - + -
107B VAL* 3.7 25.1 - - + +
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Residues in contact with ILE 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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28B LEU* 3.1 28.0 + - + +
29B GLU* 3.8 8.1 - - + +
31B ILE* 1.3 78.5 - - + +
33B GLU* 1.3 55.3 + - - +
36B HIS* 2.8 28.8 + - - -
37B THR* 3.0 41.5 + - + +
65B LEU* 4.1 13.9 - - + -
68B TRP* 3.3 42.4 - - + +
93B MET* 5.1 3.6 - - - -
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Residues in contact with GLU 33 (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 GLU 3.0 19.6 + - - +
30B LYS* 2.9 38.0 + - - +
32B ILE* 1.3 80.8 - - - +
34B GLU* 1.3 69.7 + - - +
36B HIS* 3.2 17.7 + - - -
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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 LYS* 2.9 56.0 + - - +
33B GLU* 1.3 89.5 - - - +
35B ASN* 1.3 74.5 + - - +
36B HIS* 3.5 16.1 - - - -
105B ARG* 3.4 48.2 + - + +
107B VAL* 3.9 20.4 - - + -
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Residues in contact with ASN 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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6B ILE* 3.5 21.1 - - + +
31B ILE* 2.7 39.4 + - - +
34B GLU* 1.3 84.2 - - - +
36B HIS* 1.3 75.5 + - - +
37B THR* 3.1 16.1 + - - +
99B VAL* 5.8 4.2 - - - +
104B ILE* 3.7 9.4 - - - +
105B ARG* 2.9 44.6 + - - +
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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