Contacts of the helix formed by residues 44 - 63 (chain B) in PDB entry 2CSL
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 ASP 44 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B GLY* 1.3 76.9 - - - +
45B ILE* 1.3 72.1 + - + +
46B ARG* 3.5 37.5 + - - +
47B VAL* 3.2 30.2 + - - +
48B GLN* 3.3 8.7 + - - +
114B ARG* 3.1 14.4 - - - +
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Residues in contact with ILE 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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44B ASP* 1.3 88.5 - - + +
46B ARG* 1.3 65.4 + - - +
48B GLN* 3.3 2.6 + - - +
49B THR* 2.6 51.4 + - - +
77B LEU* 4.9 6.5 - - + -
82B ASP* 3.2 66.0 - - + +
85B GLY* 4.6 4.5 - - - +
86B PHE* 3.9 13.7 - - + +
114B ARG* 3.3 14.7 - - + +
115B VAL* 5.1 6.3 - - + -
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Residues in contact with ARG 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ASP* 3.2 22.9 + - - +
45B ILE* 1.3 84.2 - - - +
47B VAL* 1.3 63.5 + - + +
50B GLU* 3.1 25.2 + - - +
84B PRO* 4.7 4.4 - - - +
85B GLY* 3.7 35.3 - - - +
88B GLU* 3.3 36.4 + - - -
89B VAL* 3.7 20.5 - - + +
92B ARG* 5.0 5.2 - - - +
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Residues in contact with VAL 47 (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 VAL* 3.7 17.6 - - + +
42B GLU 3.7 20.6 - - - +
43B GLY* 4.3 6.5 - - - -
44B ASP* 3.2 23.2 + - - +
46B ARG* 1.3 78.1 - - + +
48B GLN* 1.3 63.9 + - - +
50B GLU* 3.4 8.1 + - - +
51B ARG* 3.3 19.1 + - - +
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Residues in contact with GLN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B PRO* 3.4 24.9 - - + +
40B LEU* 4.5 8.1 - - - +
41B VAL* 2.6 28.3 + - - +
42B GLU* 3.5 11.9 - - - +
43B GLY 3.7 11.8 - - - +
44B ASP 3.3 13.0 + - - +
45B ILE 3.3 6.1 + - - +
47B VAL* 1.3 72.8 - - - +
49B THR* 1.3 66.7 + - - +
51B ARG* 3.2 5.6 + - - +
52B VAL* 3.0 24.6 + - - +
113B VAL* 4.0 5.4 - - - +
114B ARG* 2.6 45.1 + - + +
115B VAL* 4.1 8.7 - - + -
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Residues in contact with THR 49 (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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45B ILE* 2.6 45.3 + - - +
46B ARG* 4.0 1.6 - - - -
48B GLN* 1.3 72.2 - - - +
50B GLU* 1.3 58.5 + - - +
52B VAL* 3.1 3.5 + - - +
53B MSE 2.8 38.8 + - + +
86B PHE* 3.5 39.0 - - + +
89B VAL* 3.6 26.9 - - + -
90B TYR 4.5 0.9 - - - +
115B VAL* 4.0 10.9 - - + +
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Residues in contact with GLU 50 (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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46B ARG 3.1 19.1 + - - +
47B VAL* 3.6 8.6 - - - +
48B GLN 3.2 0.2 - - - -
49B THR* 1.3 76.8 - - - +
51B ARG* 1.3 62.9 + - - +
53B MSE 3.2 5.7 + - - +
54B GLU* 3.0 30.1 + - + +
89B VAL* 3.7 14.0 - - + +
92B ARG* 3.7 17.1 + - - +
93B TYR* 3.6 17.8 + - - +
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Residues in contact with ARG 51 (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 ARG 4.4 3.6 + - - -
33B PRO* 3.4 9.6 - - + -
34B LEU 3.4 33.2 - - - +
35B ALA* 4.1 6.5 - - - +
36B PRO* 3.5 30.6 - - - +
41B VAL* 3.9 21.8 - - + +
47B VAL 3.3 9.1 + - - +
48B GLN 3.2 8.1 + - - +
50B GLU* 1.3 76.4 - - - +
52B VAL* 1.3 66.7 + - - +
54B GLU* 3.2 23.6 + - - +
55B ASN* 2.6 51.4 + - - +
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Residues in contact with VAL 52 (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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31B GLN* 3.6 31.4 - - + +
32B ILE 3.7 0.4 - - - -
33B PRO* 3.7 19.1 - - + -
48B GLN 3.0 17.7 + - - +
49B THR* 3.3 9.6 - - - +
51B ARG* 1.3 76.4 - - - +
53B MSE 1.3 70.2 + - + +
55B ASN* 3.2 13.6 + - - +
56B LEU* 3.1 21.3 + - + +
115B VAL* 3.7 20.4 - - + +
117B VAL* 3.8 30.7 - - + -
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Residues in contact with MSE 53 (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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49B THR* 2.8 31.1 + - + +
50B GLU 3.5 7.2 - - - +
52B VAL* 1.3 91.5 - - + +
54B GLU* 1.3 56.6 + - - +
56B LEU* 3.2 28.0 + - + +
57B LYS* 2.9 28.2 + - - +
67B LEU* 4.8 2.4 - - - +
86B PHE* 4.4 0.7 - - + -
89B VAL* 4.1 9.4 - - + +
90B TYR* 3.8 26.0 - - + -
93B TYR* 3.5 45.9 - - + -
94B PHE* 3.8 25.6 - - - -
117B VAL* 4.0 13.2 - - + -
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Residues in contact with GLU 54 (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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50B GLU* 3.0 25.3 + - + +
51B ARG* 3.7 27.8 - - - +
53B MSE 1.3 75.7 - - - +
55B ASN* 1.3 53.6 + - - +
57B LYS* 3.1 28.8 + - - +
58B ALA* 2.8 36.2 + - - +
93B TYR* 3.1 32.1 + - - +
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Residues in contact with ASN 55 (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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9B ALA* 4.2 7.4 - - + -
10B PRO* 3.5 24.1 - - + +
31B GLN* 3.6 19.2 - - + +
32B ILE 2.9 28.3 + - - -
34B LEU 3.3 12.9 + - - -
51B ARG* 2.6 47.7 + - - +
52B VAL* 3.4 7.5 - - - +
54B GLU* 1.3 75.5 - - - +
56B LEU* 1.3 63.9 + - - +
58B ALA* 3.1 3.3 + - - +
59B VAL* 2.8 30.3 + - - +
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Residues in contact with LEU 56 (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 VAL* 4.0 14.8 - - + -
31B GLN* 3.5 25.4 - - + -
52B VAL 3.1 14.5 + - - +
53B MSE 3.4 32.1 - - + +
55B ASN* 1.3 74.3 - - - +
57B LYS* 1.3 65.3 + - - +
59B VAL* 3.7 4.5 - - - +
60B LEU* 2.8 35.4 + - + +
67B LEU* 4.5 8.1 - - + -
94B PHE* 4.6 12.1 - - + -
117B VAL* 3.7 36.6 - - + +
119B CYS* 4.1 18.2 - - - +
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Residues in contact with LYS 57 (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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53B MSE 2.9 13.4 + - - +
54B GLU* 3.2 35.9 + - - +
56B LEU* 1.3 76.0 - - - +
58B ALA* 1.3 62.6 + - - +
60B LEU* 3.8 3.0 - - - +
61B GLU* 3.0 56.9 + - + +
67B LEU* 3.9 33.5 - - + +
93B TYR* 5.1 4.5 - - + -
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Residues in contact with ALA 58 (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 THR* 4.2 4.0 + - - +
8B ARG* 3.6 46.8 - - + +
9B ALA* 4.2 2.5 - - + -
54B GLU 2.8 19.3 + - - +
55B ASN 3.5 4.5 - - - +
57B LYS* 1.3 74.8 - - - +
59B VAL* 1.3 63.3 + - - +
61B GLU* 4.0 8.3 - - - +
62B ALA* 3.0 25.9 + - - +
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Residues in contact with VAL 59 (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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4B VAL* 3.7 4.1 - - + +
6B THR* 4.3 7.9 - - + -
9B ALA* 3.8 19.5 - - + -
18B GLN* 3.7 19.3 - - + +
19B ALA* 3.4 31.6 - - + -
28B VAL* 3.7 19.3 - - + -
31B GLN* 3.9 17.9 - - - +
55B ASN 2.8 24.8 + - - +
56B LEU 3.7 3.6 - - - +
58B ALA* 1.3 72.8 - - - +
60B LEU* 1.3 62.9 + - - +
62B ALA* 3.4 3.5 + - - +
63B ALA* 3.2 19.9 + - - +
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Residues in contact with LEU 60 (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 VAL* 4.5 6.7 - - + -
28B VAL* 3.7 28.0 - - + -
56B LEU* 2.8 26.1 + - + +
57B LYS 3.8 3.1 - - - +
59B VAL* 1.3 69.1 - - - +
61B GLU* 1.3 66.0 + - - +
63B ALA* 2.9 17.4 + - - +
65B SER* 3.0 23.2 + - - +
66B GLY* 3.6 24.5 - - - +
67B LEU* 3.9 15.9 - - + +
70B VAL* 3.5 26.0 - - + -
119B CYS* 4.4 8.1 - - - -
121B ALA* 3.9 24.7 - - + -
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Residues in contact with GLU 61 (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 ARG* 5.7 4.3 - - - -
57B LYS* 3.0 53.4 + - + +
58B ALA* 4.0 6.5 - - - +
60B LEU* 1.3 75.7 - - - +
62B ALA* 1.3 55.8 + - - +
64B GLY* 2.6 28.4 + - - -
65B SER 3.5 15.3 - - - +
66B GLY* 4.9 5.6 - - - -
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Residues in contact with ALA 62 (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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4B VAL* 3.9 13.5 - - + +
5B LYS 4.5 4.6 - - - +
6B THR* 3.5 29.4 - - + +
58B ALA 3.0 19.0 + - - +
59B VAL 3.6 6.3 - - - +
61B GLU* 1.3 76.3 - - - +
63B ALA* 1.3 57.5 + - - +
64B GLY 3.2 1.1 + - - -
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Residues in contact with ALA 63 (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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4B VAL* 3.5 30.1 - - + -
21B LYS* 3.4 31.3 + - + -
26B VAL* 3.9 24.7 - - + +
59B VAL 3.2 8.1 + - - +
60B LEU 2.9 10.0 + - - +
61B GLU 2.9 1.2 - - - -
62B ALA* 1.3 76.8 - - - +
64B GLY* 1.3 62.0 + - - +
65B SER* 3.3 2.4 + - - -
123B ALA* 5.2 1.6 - - - +
124B GLU 5.8 0.2 + - - -
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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
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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