Contacts of the helix formed by residues 44 - 64 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A GLY* 1.3 76.5 - - - +
45A ILE* 1.3 69.5 + - + +
46A ARG* 3.7 24.6 + - - +
47A VAL* 3.1 32.9 + - - +
48A GLN* 3.2 8.3 + - - +
114A ARG* 3.6 12.1 - - - +
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ASP* 1.3 75.0 - - + +
46A ARG* 1.3 62.9 + - - +
48A GLN 3.1 0.9 + - - +
49A THR* 2.5 43.6 + - - +
77A LEU* 4.9 0.4 - - + -
81A GLU 5.1 0.7 - - - +
82A ASP* 2.8 74.7 - - + +
84A PRO* 5.6 0.2 - - + -
85A GLY* 3.2 25.1 - - - +
86A PHE* 4.2 6.3 - - + +
114A ARG* 4.1 13.8 - - + +
115A VAL* 3.8 25.6 - - + -
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Residues in contact with ARG 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASP* 3.2 20.4 + - - +
45A ILE* 1.3 84.7 - - + +
47A VAL* 1.3 62.9 + - + +
50A GLU* 3.1 26.7 + - - +
84A PRO* 5.0 2.6 - - - +
85A GLY* 3.6 35.2 - - - +
88A GLU* 2.4 35.7 + - - +
89A VAL* 3.8 21.3 - - + +
92A ARG* 5.2 6.8 - - - +
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Residues in contact with VAL 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A VAL* 3.6 24.9 - - + +
42A GLU 3.7 12.6 - - - +
43A GLY* 4.3 4.0 - - - -
44A ASP* 3.1 27.8 + - - +
46A ARG* 1.3 77.2 - - + +
48A GLN* 1.3 63.4 + - - +
50A GLU* 3.5 7.1 + - - +
51A ARG* 3.4 17.8 + - - +
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Residues in contact with GLN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A PRO* 3.2 28.6 - - + +
40A LEU* 5.4 2.0 - - - +
41A VAL* 3.5 22.0 - - - +
42A GLU* 4.4 1.9 - - - +
43A GLY 3.2 18.5 + - - +
44A ASP 3.2 7.6 + - - +
45A ILE 3.1 4.4 + - - +
47A VAL* 1.3 73.2 - - - +
49A THR* 1.3 68.5 + - - +
50A GLU 3.0 1.6 - - - -
51A ARG* 3.0 5.8 + - - +
52A VAL* 3.0 24.9 + - - +
113A VAL* 4.0 6.6 - - - +
114A ARG* 2.8 56.7 + - + +
115A VAL* 4.1 2.4 - - + +
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Residues in contact with THR 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ILE 2.5 25.4 + - - -
46A ARG 4.1 0.2 - - - -
48A GLN* 1.3 72.2 - - - +
50A GLU* 1.3 57.4 + - - +
52A VAL* 3.2 10.7 + - - +
53A MSE 2.9 35.8 + - + +
86A PHE* 3.3 49.6 - - + +
89A VAL* 3.5 30.1 - - + -
90A TYR 4.4 1.1 - - - +
115A VAL* 3.6 14.0 - - - +
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Residues in contact with GLU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ARG 3.1 17.3 + - - +
47A VAL* 3.6 7.6 - - - +
48A GLN 3.0 0.6 - - - -
49A THR* 1.3 77.0 - - - +
51A ARG* 1.3 65.3 + - - +
53A MSE 3.3 3.8 + - - +
54A GLU* 3.0 28.9 + - + +
89A VAL* 3.8 12.5 - - + +
92A ARG* 3.2 20.9 + - - -
93A TYR* 3.6 20.1 + - + +
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Residues in contact with ARG 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG 4.6 4.6 + - - -
33A PRO* 3.6 23.3 - - + -
34A LEU 3.4 8.5 + - - -
35A ALA* 3.7 6.0 - - - +
36A PRO* 3.2 32.0 - - - +
41A VAL* 3.6 28.3 - - + -
47A VAL 3.4 8.9 + - - +
48A GLN 3.0 9.2 + - - +
50A GLU* 1.3 76.9 - - - +
52A VAL* 1.3 54.1 + - - +
54A GLU* 3.0 36.3 + - - +
55A ASN* 2.5 78.5 + - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 3.6 25.1 - - + +
32A ILE 3.7 3.8 - - - -
33A PRO* 3.6 28.7 - - + -
48A GLN 3.0 14.5 + - - +
49A THR* 3.3 9.2 - - - +
51A ARG* 1.3 75.8 - - - +
53A MSE 1.3 70.2 + - + +
55A ASN* 3.1 12.0 + - - +
56A LEU* 2.9 23.3 + - + +
115A VAL* 4.1 14.8 - - + +
117A VAL* 3.8 27.6 - - + -
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Residues in contact with MSE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A THR* 2.9 30.5 + - + +
50A GLU 3.6 4.5 - - - +
51A ARG 3.2 0.4 - - - -
52A VAL* 1.3 86.9 - - + +
54A GLU* 1.3 57.3 + - - +
56A LEU* 3.2 31.9 + - + +
57A LYS* 2.9 30.5 + - - +
67A LEU* 4.7 3.5 - - - +
86A PHE* 4.6 0.4 - - + -
89A VAL 4.1 5.6 - - - +
90A TYR* 4.1 20.2 - - + -
93A TYR* 3.4 46.0 - - + -
94A PHE* 3.6 26.9 - - - -
117A VAL* 4.0 16.2 - - + -
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 4.9 3.3 + - - +
50A GLU* 3.0 26.3 + - + +
51A ARG* 3.0 34.2 + - - +
53A MSE 1.3 75.7 - - - +
55A ASN* 1.3 62.2 + - - +
57A LYS* 3.4 23.1 + - - +
58A ALA* 3.0 23.6 + - - +
93A TYR* 2.8 32.3 + - - +
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Residues in contact with ASN 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG 5.1 0.4 - - - -
9A ALA* 4.1 6.0 - - - -
10A PRO* 3.0 23.3 - - + +
31A GLN* 3.3 20.7 - - + +
32A ILE 2.9 28.5 + - - -
34A LEU 3.3 10.7 + - - -
51A ARG* 2.5 52.6 + - - +
52A VAL* 3.3 7.0 - - - +
54A GLU* 1.3 69.4 - - - +
56A LEU* 1.3 67.4 + - - +
58A ALA* 3.0 12.6 + - - +
59A VAL* 3.0 20.1 + - - +
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Residues in contact with LEU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A VAL* 4.0 16.4 - - + -
31A GLN* 3.7 16.5 - - + +
52A VAL* 2.9 17.5 + - + +
53A MSE 3.5 42.8 - - + +
55A ASN* 1.3 72.1 - - - +
57A LYS* 1.3 58.2 + - - +
59A VAL* 3.2 5.1 + - - +
60A LEU* 2.9 44.1 + - + +
67A LEU* 4.5 3.1 - - + -
94A PHE* 4.6 10.8 - - + -
117A VAL* 3.7 37.5 - - + +
119A CYS* 4.1 16.4 - - - +
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Residues in contact with LYS 57 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A ARG* 5.2 7.8 - - - +
53A MSE 2.9 16.4 + - - +
54A GLU* 3.4 31.1 + - - +
56A LEU* 1.3 77.9 - - - +
58A ALA* 1.3 62.5 + - - +
60A LEU* 4.0 3.2 - - - +
61A GLU* 3.1 55.5 + - + +
66A GLY* 5.6 0.2 - - - -
67A LEU* 3.8 36.3 - - + +
93A TYR* 4.9 5.8 - - + -
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Residues in contact with ALA 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A THR* 4.3 3.2 + - - +
8A ARG* 3.4 65.9 + - + +
9A ALA* 4.1 2.5 - - + -
54A GLU 3.0 12.8 + - - +
55A ASN 3.0 6.9 + - - +
57A LYS* 1.3 75.4 - - - +
59A VAL* 1.3 57.7 - - - +
61A GLU* 3.5 2.7 + - - +
62A ALA* 3.0 29.0 + - - +
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Residues in contact with VAL 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 3.8 4.6 - - + +
6A THR* 4.3 8.3 - - + -
9A ALA* 3.8 19.3 - - + -
18A GLN* 3.7 26.9 - - + +
19A ALA* 3.4 31.4 - - + -
28A VAL* 4.1 11.4 - - + -
31A GLN* 4.4 13.9 - - - +
55A ASN 3.0 16.2 + - - +
56A LEU* 3.6 6.1 - - - +
58A ALA* 1.3 74.3 - - - +
60A LEU* 1.3 65.4 + - - +
62A ALA* 3.2 4.5 + - - +
63A ALA* 3.0 20.3 + - - +
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Residues in contact with LEU 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A VAL* 4.6 4.5 - - + -
28A VAL* 3.8 25.1 - - + -
56A LEU* 2.9 28.7 + - + +
57A LYS 4.0 2.7 - - - +
59A VAL* 1.3 76.9 - - - +
61A GLU* 1.3 61.1 + - - +
63A ALA* 3.1 12.9 + - - +
64A GLY 3.2 0.3 + - - -
65A SER* 2.9 31.1 + - - +
66A GLY* 3.8 17.3 - - - +
67A LEU* 4.0 17.0 - - + +
70A VAL* 3.5 23.8 - - + -
119A CYS* 4.3 6.5 - - - -
121A ALA* 3.6 31.0 - - + -
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Residues in contact with GLU 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 2.9 35.8 + - - +
57A LYS* 3.1 46.1 + - + +
58A ALA 3.8 2.9 - - - +
59A VAL 3.2 0.2 - - - -
60A LEU* 1.3 69.9 - - - +
62A ALA* 1.3 58.8 + - - +
63A ALA 2.9 4.7 - - - -
64A GLY* 2.8 21.3 + - - -
65A SER 3.5 15.2 + - - +
66A GLY* 4.9 5.4 - - - -
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Residues in contact with ALA 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 3.7 16.1 - - + +
5A LYS 4.4 3.8 - - - +
6A THR* 3.7 27.4 - - + +
21A LYS* 4.9 4.2 + - - -
58A ALA 3.0 18.7 + - - +
59A VAL 3.2 5.4 + - - +
61A GLU* 1.3 75.4 - - - +
63A ALA* 1.3 58.2 + - - +
64A GLY 3.3 0.6 + - - -
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Residues in contact with ALA 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 3.9 17.3 - - + -
19A ALA* 5.3 0.2 - - + -
21A LYS* 3.1 36.0 + - + +
26A VAL* 3.7 36.5 - - + +
59A VAL 3.0 11.8 + - - +
60A LEU 3.3 11.2 - - - +
61A GLU 2.9 1.0 - - - -
62A ALA* 1.3 78.0 - - - +
64A GLY* 1.3 58.2 + - - +
65A SER* 3.5 0.4 - - - -
123A ALA* 5.5 1.9 - - - +
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Residues in contact with GLY 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 5.1 1.1 - - - -
61A GLU 2.8 12.0 + - - -
62A ALA 3.3 1.0 + - - -
63A ALA* 1.3 81.1 - - - +
65A SER* 1.3 60.4 + - - +
123A ALA* 5.6 0.2 - - - -
124A GLU* 3.0 33.0 + - - +
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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
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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