Contacts of the helix formed by residues 45 - 61 (chain A) in PDB entry 6B3I
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 THR 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A ARG* 1.3 75.7 - - - +
46A SER* 1.3 64.6 + - - +
47A ASP* 3.7 7.0 + - - +
48A GLU* 2.8 43.1 + - - +
49A ARG* 3.1 24.8 + - - +
277A GLU* 3.3 13.2 - - + +
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Residues in contact with SER 46 (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 THR* 1.3 72.0 - - - +
47A ASP* 1.3 61.8 + - - +
49A ARG* 3.5 28.3 + - - +
50A GLN* 3.1 26.8 + - - +
85A ASP 4.6 3.5 + - - -
86A HIS* 4.4 10.7 - - - -
87A PRO* 4.2 21.7 - - - +
277A GLU* 2.6 32.8 + - - -
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Residues in contact with ASP 47 (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 THR* 3.2 7.4 + - - +
46A SER* 1.3 78.1 - - - +
48A GLU* 1.3 65.6 + - + +
50A GLN* 3.3 8.9 + - - +
51A GLN* 2.9 49.4 + - - +
86A HIS* 6.4 0.2 - - - -
277A GLU* 4.5 0.8 + - - -
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Residues in contact with GLU 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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43A GLY 4.7 1.4 - - - +
44A ARG* 3.5 17.6 - - + -
45A THR* 2.8 50.4 + - - +
47A ASP* 1.3 82.7 - - + +
49A ARG* 1.3 61.1 + - - +
51A GLN* 3.2 11.1 + - - +
52A ILE* 3.2 17.5 + - - +
14B PHE* 3.4 60.3 - - + +
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Residues in contact with ARG 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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40A ILE* 5.4 2.2 - - + +
41A LEU* 3.6 29.0 + - + +
44A ARG* 3.3 30.3 + - + +
45A THR* 3.1 10.3 + - - +
46A SER* 3.5 39.5 + - - +
48A GLU* 1.3 74.0 - - - +
50A GLN* 1.3 60.6 + - + +
51A GLN 3.3 0.2 - - - -
52A ILE* 3.7 18.9 - - + +
53A LYS* 3.1 26.0 + - - +
83A LEU* 2.6 59.0 + - - +
84A LEU* 4.4 20.6 - - + +
85A ASP 4.9 2.0 + - - -
276A ALA* 5.5 7.5 - - - +
277A GLU* 4.6 4.9 + - - +
314A LEU* 5.6 2.8 - - - +
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Residues in contact with GLN 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 SER* 3.1 25.3 + - - +
47A ASP* 3.5 11.4 - - - +
48A GLU 3.2 0.4 - - - -
49A ARG* 1.3 78.7 - - + +
51A GLN* 1.3 61.7 + - + +
53A LYS* 3.4 23.4 + - - +
54A GLN* 3.5 34.6 + - - +
83A LEU 5.6 0.2 + - - -
84A LEU* 3.0 28.9 + - - +
85A ASP 3.9 0.8 + - - -
86A HIS* 3.5 54.5 + - + +
89A GLU* 5.5 0.6 + - - -
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Residues in contact with GLN 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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47A ASP* 2.9 35.4 + - - +
48A GLU* 3.2 7.5 + - - +
50A GLN* 1.3 77.0 - - + +
52A ILE* 1.3 53.6 + - - +
54A GLN* 3.3 8.3 + - - +
55A LYS* 2.7 36.2 + - - +
14B PHE* 3.2 28.1 - - - -
16B VAL* 3.8 17.6 - - + +
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Residues in contact with ILE 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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40A ILE* 4.2 14.4 - - + -
44A ARG* 4.2 6.7 - - + -
48A GLU 3.2 19.3 + - - +
49A ARG* 3.7 16.8 - - + +
50A GLN 3.4 0.6 - - - -
51A GLN* 1.3 76.2 - - - +
53A LYS* 1.3 58.1 + - - +
55A LYS* 3.7 1.4 - - - +
56A TYR* 2.8 31.3 + - + +
64A LEU* 4.9 3.1 - - + -
14B PHE* 4.3 4.0 - - + -
16B VAL* 3.9 17.9 - - + +
19B ASP* 3.6 31.4 - - + +
20B ALA* 3.8 20.0 - - + +
23B LEU* 3.7 27.8 - - + -
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Residues in contact with LYS 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 ARG 3.1 16.3 + - - +
50A GLN* 3.4 27.9 + - - +
51A GLN 3.2 0.4 - - - -
52A ILE* 1.3 78.0 - - - +
54A GLN* 1.3 62.8 + - + +
56A TYR* 3.8 2.9 - - - +
57A LYS* 3.4 20.8 + - - +
63A GLU* 4.0 15.7 - - - +
64A LEU* 4.3 28.7 + - + +
65A GLU* 4.1 32.0 + - + +
84A LEU* 2.7 35.5 + - + +
85A ASP* 4.6 3.8 + - - +
89A GLU* 5.7 2.0 + - - -
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Residues in contact with GLN 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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50A GLN* 3.5 21.4 + - - +
51A GLN* 3.3 9.5 + - - +
53A LYS* 1.3 79.5 - - + +
55A LYS* 1.3 65.2 + - - +
57A LYS* 3.4 7.3 + - - +
58A ALA* 3.2 22.5 + - - +
63A GLU* 5.5 0.4 - - - -
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Residues in contact with LYS 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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51A GLN 2.7 23.3 + - - +
52A ILE* 3.9 3.4 - - - +
54A GLN* 1.3 69.5 - - - +
56A TYR* 1.3 65.0 + - - +
58A ALA* 3.4 8.3 + - + +
59A THR* 3.0 41.2 + - - +
16B VAL* 3.7 31.5 - - + +
17B ASP* 3.2 34.2 + - - +
20B ALA* 4.4 7.6 - - + -
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Residues in contact with TYR 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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52A ILE 2.8 17.6 + - - +
53A LYS 3.8 5.4 - - - +
55A LYS* 1.3 78.4 - - - +
57A LYS* 1.3 62.5 + - - +
60A TYR* 3.0 37.4 + + + +
61A GLY 3.8 0.5 + - - -
62A LYS* 3.1 29.7 - - + +
64A LEU* 4.0 36.1 - - + -
67A VAL* 4.1 30.2 - - + +
20B ALA* 3.5 22.1 - - + +
23B LEU* 4.2 4.5 - - + -
24B ASN* 3.3 52.5 + - + -
27B CYS* 4.2 4.9 - - - +
28B LYS* 5.3 1.6 - - - +
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Residues in contact with LYS 57 (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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53A LYS 3.4 6.5 + - - +
54A GLN* 3.8 9.4 - - - +
55A LYS 3.3 0.6 - - - -
56A TYR* 1.3 77.8 - - - +
58A ALA* 1.3 58.1 + - - +
61A GLY* 3.1 37.1 + - - -
62A LYS 3.6 27.1 + - - +
63A GLU* 3.2 39.0 - - - +
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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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54A GLN 3.2 16.0 + - - +
55A LYS* 3.4 11.4 + - + +
56A TYR 3.2 0.2 - - - -
57A LYS* 1.3 80.0 - - - +
59A THR* 1.3 63.5 + - - +
61A GLY* 4.5 1.4 + - - -
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Residues in contact with THR 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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55A LYS* 3.0 33.1 + - - +
58A ALA* 1.3 79.4 - - - +
60A TYR* 1.3 93.2 + - + +
61A GLY 3.7 0.2 - - - -
17B ASP* 5.1 1.9 + - - -
20B ALA* 5.9 0.6 - - - +
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Residues in contact with TYR 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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56A TYR* 3.0 43.0 + + + +
59A THR* 1.3 102.7 - - + +
61A GLY* 1.3 63.7 + - - +
62A LYS* 3.2 16.5 + - + +
20B ALA* 3.5 21.7 - - + -
21B LYS* 3.3 31.5 - - - +
24B ASN* 3.3 38.4 + - + +
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Residues in contact with GLY 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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56A TYR 3.8 0.4 + - - -
57A LYS* 3.1 37.2 + - - -
58A ALA 4.4 1.2 + - - -
59A THR 3.7 1.2 - - - -
60A TYR* 1.3 76.3 - - - +
62A LYS* 1.3 62.0 + - - +
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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