Contacts of the helix formed by residues 45 - 57 (chain A) in PDB entry 5B6N
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 PRO 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 THR* 1.3 89.8 - - + +
46A VAL* 1.3 62.5 + - + +
48A THR* 3.7 4.7 - - - +
49A THR* 3.3 22.2 + - - +
176B ALA* 6.2 0.4 - - + -
188B MET* 3.6 33.2 - - + +
189B VAL 3.7 20.6 - - - +
190B LEU* 5.2 0.2 - - - -
191B PRO* 3.5 26.0 - - + -
217B TYR* 3.4 23.5 - - + +
218B LEU* 3.8 13.7 - - + +
219B ARG 4.6 0.2 - - - +
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Residues in contact with VAL 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A THR* 3.3 3.9 - - + +
45A PRO* 1.3 79.8 - - + +
47A CSD 1.3 66.6 + - - +
48A THR 3.0 4.5 - - - -
49A THR* 2.2 28.2 + - - -
50A GLU* 3.0 10.9 + - + +
132A ARG* 3.4 28.9 - - - +
151A ALA 4.7 0.7 - - - +
154A GLY* 4.3 6.3 - - - +
176B ALA* 3.6 30.7 - - + -
177B THR 3.4 21.5 - - - +
178B PRO* 3.8 7.2 - - + -
188B MET* 4.0 16.4 - - + -
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Residues in contact with CSD 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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39A HIS* 3.6 25.4 - - + -
40A PRO* 3.4 15.5 - - - +
41A ARG 3.2 18.3 + - - +
44A THR* 3.4 16.8 + - - +
46A VAL* 1.3 75.1 + - - +
48A THR* 1.3 58.2 + - - +
50A GLU* 3.7 9.4 - - - -
51A LEU* 3.3 19.1 + - + +
82A TRP* 3.2 32.4 - - + -
132A ARG* 2.4 39.4 + - - -
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Residues in contact with THR 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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44A THR 2.1 34.0 + - - -
45A PRO* 3.7 8.6 - - - +
46A VAL 3.0 0.2 - - - -
47A CSD 1.3 79.0 + - - -
49A THR* 1.3 64.4 + - - +
50A GLU 3.1 1.1 - - - -
52A GLY* 3.3 15.9 + - - -
82A TRP* 3.9 11.3 + - - +
85A ASP 4.5 5.4 - - - +
86A ILE* 3.6 21.9 - - + +
89A TYR* 3.4 29.8 - - + -
211B LEU* 4.9 1.8 - - + -
217B TYR* 3.7 15.5 - - + +
218B LEU* 4.0 16.4 - - + -
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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 PRO 3.3 16.8 - - - +
46A VAL* 2.2 30.3 + - - -
48A THR* 1.3 78.9 - - - +
50A GLU* 1.3 58.2 + - - +
53A ARG* 3.2 16.1 + - - +
89A TYR* 3.5 31.3 + - + +
178B PRO* 3.6 17.3 - - + +
179B VAL* 3.1 38.6 + - - +
188B MET* 4.7 3.4 - - + -
218B LEU* 5.2 0.4 - - + -
220B TYR* 4.1 11.4 - - + +
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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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37A PHE* 5.1 0.5 - - - -
39A HIS* 4.8 1.4 - - - +
46A VAL* 3.0 18.8 + - + +
47A CSD 3.9 7.9 - - - +
48A THR 3.1 0.4 - - - -
49A THR* 1.3 77.7 + - - +
51A LEU* 1.3 68.8 + - + +
52A GLY 3.1 1.6 - - - -
53A ARG* 2.9 20.1 + - - +
54A ALA* 3.0 12.9 + - - +
132A ARG* 3.1 30.2 + - - +
154A GLY* 3.7 1.9 - - - -
155A ARG* 2.8 57.1 + - - -
157A PHE* 4.3 10.3 - - + -
179B VAL* 3.5 21.8 - - + -
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Residues in contact with LEU 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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37A PHE* 3.8 23.8 - - + -
39A HIS* 3.7 35.4 - - + +
47A CSD 3.3 20.3 + - - +
50A GLU* 1.3 87.0 - - + +
52A GLY* 1.3 59.7 + - - +
54A ALA* 3.3 7.0 + - - -
55A ALA* 3.2 20.4 + - - +
70A ALA* 4.5 2.0 - - + -
82A TRP* 3.5 25.4 - - + -
86A ILE* 4.1 13.1 - - + +
98A LEU* 4.8 6.5 - - + -
100A PHE* 3.5 25.2 - - + -
102A ILE* 4.4 11.9 - - + -
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Residues in contact with GLY 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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48A THR 3.3 17.2 + - - -
49A THR 4.2 0.4 - - - -
50A GLU 3.1 1.0 - - - -
51A LEU* 1.3 77.5 - - - +
53A ARG* 1.3 62.2 + - - +
55A ALA* 3.4 1.7 + - - +
56A LYS* 3.3 18.5 + - - +
86A ILE* 3.9 13.1 - - - +
89A TYR* 4.3 8.1 - - - -
90A ASN* 3.2 30.3 + - - -
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Residues in contact with ARG 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 3.2 15.7 + - - +
50A GLU* 2.9 10.1 + - - +
52A GLY* 1.3 76.2 - - - +
54A ALA* 1.3 57.3 + - - +
55A ALA 3.1 1.8 - - - -
56A LYS* 3.4 31.4 + - - +
57A LEU* 3.1 57.0 + - - +
89A TYR* 5.0 0.2 - - - -
157A PHE* 3.9 22.3 - - + +
158A ASP* 2.4 34.1 + - - -
179B VAL* 4.1 9.4 - - + -
180B ASP* 3.4 22.3 + - - +
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Residues in contact with ALA 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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37A PHE* 4.2 6.5 - - + -
50A GLU 3.0 9.2 + - - +
51A LEU* 3.5 12.6 - - - +
52A GLY 3.2 0.2 - - - -
53A ARG* 1.3 76.4 - - - +
55A ALA* 1.3 58.0 + - - +
56A LYS 3.4 0.2 - - - -
57A LEU* 3.9 4.6 - - - -
58A ALA* 3.2 17.8 + - - +
68A LEU* 3.5 20.0 - - + +
100A PHE* 3.5 15.0 - - + -
157A PHE* 3.7 33.9 - - + -
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Residues in contact with ALA 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 LEU 3.2 14.3 + - - +
52A GLY* 3.8 8.5 - - - +
53A ARG 3.1 0.4 - - - -
54A ALA* 1.3 77.9 - - - +
56A LYS* 1.3 62.0 + - - +
57A LEU 3.2 1.6 - - - -
58A ALA* 3.6 7.0 - - - +
59A PRO* 4.1 4.0 - - - +
86A ILE* 5.2 0.2 - - + -
87A ASN* 5.7 0.9 - - - +
90A ASN* 4.8 6.1 - - - +
98A LEU* 4.5 9.0 - - + -
99A PRO* 3.5 39.5 - - + +
100A PHE* 3.6 9.2 - - + -
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Residues in contact with LYS 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 GLY 3.3 17.0 + - - +
53A ARG* 3.4 37.6 + - - +
55A ALA* 1.3 77.8 - - - +
57A LEU* 1.3 65.1 + - + +
58A ALA 3.3 0.2 - - - -
59A PRO* 3.5 11.6 - - - +
60A GLU* 5.0 3.8 - - - +
89A TYR* 6.4 1.6 - - - -
90A ASN* 3.9 27.1 - - + +
92A GLU* 5.2 6.5 - - - +
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Residues in contact with LEU 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 ARG* 3.1 53.5 + - - +
54A ALA* 3.9 3.8 - - - +
55A ALA 3.2 0.2 - - - -
56A LYS* 1.3 80.8 - - + +
58A ALA* 1.3 63.7 + - - +
59A PRO* 3.3 4.0 - - - -
60A GLU* 2.9 34.7 + - + +
61A PHE* 3.0 32.7 + - + -
157A PHE* 3.7 31.4 - - + +
158A ASP* 4.3 1.8 - - - +
161A LEU* 4.8 9.2 - - + -
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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
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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