Contacts of the helix formed by residues 49 - 63 (chain A) in PDB entry 5BTL
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 LYS 49 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A ARG 3.3 20.0 - - - +
40A ALA* 3.1 22.1 + - - +
41A LEU* 4.1 14.8 - - - +
42A PRO* 4.2 3.6 - - + -
47A GLY 5.7 0.2 - - - +
48A LEU* 1.3 75.2 - - - +
50A PRO* 1.3 79.8 - - + +
51A VAL* 3.3 8.3 - - + +
52A HIS* 3.2 36.0 + - + +
53A ARG* 3.1 21.7 + - - +
178A SER* 3.9 15.0 - - - +
179A GLY 2.8 28.2 + - - +
180A GLY* 3.6 4.0 - - - -
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Residues in contact with PRO 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 VAL 4.9 2.5 - - - +
38A GLY* 3.5 33.7 - - - +
39A ARG* 3.9 16.8 - - - +
41A LEU 4.7 4.3 - - - +
48A LEU 4.8 0.4 - - - +
49A LYS* 1.3 89.4 - - + +
51A VAL* 1.3 57.4 + - - +
53A ARG* 3.4 17.4 + - - +
54A ARG* 2.9 57.7 + - - +
85A HIS* 5.0 3.4 - - + -
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Residues in contact with VAL 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ARG 5.5 2.5 - - - +
49A LYS* 4.6 9.0 - - + -
50A PRO* 1.3 76.3 - - - +
52A HIS* 1.3 83.2 + - + +
54A ARG* 3.3 1.4 + - - +
55A VAL* 2.9 45.7 + - + +
85A HIS* 3.6 39.8 - - + +
92A ILE* 4.6 7.2 - - + -
95A SER* 3.9 28.9 - - - +
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Residues in contact with HIS 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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47A GLY 5.2 1.9 + - - -
48A LEU* 3.8 22.8 - - + +
49A LYS* 3.2 57.4 + - + +
51A VAL* 1.3 89.8 - - + +
53A ARG* 1.3 62.1 + - - +
55A VAL* 3.3 1.2 + - - +
56A LEU* 3.0 31.9 + - - +
95A SER* 4.7 10.8 + - - -
98A ARG* 5.4 10.7 + - - -
99A MET* 3.9 34.9 - - + +
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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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43A GLU* 3.4 15.4 - - - +
46A ASP* 2.8 32.3 + - - -
48A LEU* 2.9 36.7 + - + +
49A LYS 3.1 4.6 + - - +
50A PRO* 3.7 26.6 - - - +
52A HIS* 1.3 77.9 - - - +
54A ARG* 1.3 59.7 + - + +
56A LEU* 3.6 1.6 + - - +
57A TYR* 3.0 28.8 + - - +
163A PRO* 3.5 20.4 - - + +
164A THR 3.4 26.1 + - - -
165A VAL* 3.6 9.6 - - - +
166A LEU* 3.6 23.1 - - + +
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Residues in contact with ARG 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 PRO* 2.9 34.0 + - - +
51A VAL* 3.9 4.0 - - - +
53A ARG* 1.3 78.0 - - + +
55A VAL* 1.3 59.8 + - - +
57A TYR* 3.9 3.8 - - - +
58A ALA* 2.9 30.8 + - - +
80A THR* 3.7 10.8 - - + +
84A TYR* 3.2 38.8 + - + -
85A HIS* 3.2 31.3 + - + -
86A PRO* 4.1 8.1 - - - +
87A HIS* 5.1 2.4 + - - -
156A TYR* 5.8 4.0 - - - +
162A GLU* 2.9 42.8 + - - +
163A PRO* 6.5 0.4 - - + -
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Residues in contact with VAL 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 VAL* 2.9 28.6 + - + +
52A HIS 3.8 2.9 - - - +
54A ARG* 1.3 76.1 - - - +
56A LEU* 1.3 63.5 + - - +
58A ALA* 3.2 2.6 + - - +
59A MET* 3.0 32.8 + - + +
80A THR* 3.5 25.5 + - + +
92A ILE* 4.1 23.1 - - + +
95A SER* 5.1 0.7 - - - -
96A LEU* 3.9 28.5 - - + +
99A MET* 3.8 23.3 - - + -
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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
----------------------------------------------------------
48A LEU* 4.0 22.4 - - + -
52A HIS 3.0 22.4 + - - +
53A ARG 4.0 2.9 - - - +
55A VAL* 1.3 77.7 - - + +
57A TYR* 1.3 56.6 + - - +
59A MET* 3.4 3.1 + - - +
60A PHE* 2.9 29.6 + - - +
99A MET* 4.3 15.7 - - + -
109A LEU* 3.9 43.5 - - + +
110A VAL* 4.4 5.4 - - + -
134A LEU* 3.4 30.7 - - + +
138A ALA* 4.5 3.6 - - + -
141A MET* 5.3 6.3 - - + -
142A LEU* 4.5 6.1 - - + -
166A LEU* 4.3 12.6 - - + -
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Residues in contact with TYR 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 3.0 19.4 + - - +
54A ARG* 4.1 4.0 - - - +
56A LEU* 1.3 74.0 - - - +
58A ALA* 1.3 57.0 + - - +
60A PHE* 3.5 21.9 - + - +
61A ASP* 2.8 49.4 + - + +
84A TYR* 3.6 34.8 - + - -
142A LEU* 4.2 7.1 - - + +
145A ILE* 3.9 27.6 - - + -
152A PHE* 3.5 24.1 - + - -
161A GLN 4.4 6.4 + - - -
163A PRO* 3.7 31.2 - - + -
166A LEU* 4.9 0.7 - - + -
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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 ARG 2.9 19.5 + - - +
55A VAL 3.2 1.3 + - - +
57A TYR* 1.3 77.4 - - - +
59A MET* 1.3 53.2 + - - +
61A ASP* 3.5 2.1 + - - +
62A SER* 2.7 37.9 + - - -
64A PHE* 5.5 0.2 - - - -
76A SER* 4.4 1.6 - - - +
79A GLU* 4.1 8.4 - - + +
80A THR* 3.2 37.9 - - - +
84A TYR* 3.9 17.3 - - + -
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Residues in contact with MET 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 VAL* 3.0 26.7 + - + +
56A LEU* 3.7 4.5 - - - +
58A ALA* 1.3 74.8 - - - +
60A PHE* 1.3 61.3 + - - +
62A SER 3.3 0.9 + - - -
63A GLY 3.1 3.6 + - - -
64A PHE* 2.8 43.7 + - + +
76A SER* 3.3 28.7 - - - +
96A LEU* 4.0 17.7 - - - -
110A VAL* 4.5 10.3 - - + -
132A ALA* 3.9 10.5 - - + +
133A ARG* 3.3 47.3 - - - +
134A LEU* 3.6 20.0 - - + +
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Residues in contact with PHE 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 LEU 2.9 17.5 + - - +
57A TYR* 3.5 23.8 - + - +
58A ALA 3.2 0.2 - - - -
59A MET* 1.3 77.9 - - - +
61A ASP* 1.3 63.8 + - - +
63A GLY 3.0 13.0 + - - -
65A ARG* 2.9 62.4 + - - +
134A LEU* 3.6 6.1 - - + -
139A MET* 4.1 17.0 - - - -
142A LEU* 3.6 37.5 - - + -
144A GLU 6.0 0.2 - - - -
145A ILE* 3.7 27.4 - - + -
146A ASP* 5.6 8.7 - - + -
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Residues in contact with ASP 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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57A TYR* 2.8 42.6 + - + +
58A ALA* 4.0 3.6 - - - +
60A PHE* 1.3 78.9 - - - +
62A SER* 1.3 59.8 + - - +
63A GLY* 3.1 0.9 + - - -
65A ARG* 4.7 2.9 + - - +
79A GLU* 5.2 5.6 - - - +
84A TYR* 3.7 16.9 + - - +
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Residues in contact with SER 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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58A ALA 2.7 22.1 + - - -
59A MET 3.7 4.3 - - - -
61A ASP* 1.3 76.6 - - - +
63A GLY* 1.3 60.4 + - - +
64A PHE* 3.6 35.3 + - - -
68A ARG* 5.9 1.0 + - - -
79A GLU* 3.3 31.8 + - - +
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Residues in contact with GLY 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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59A MET 3.7 0.2 - - - -
60A PHE 3.0 15.5 + - - -
61A ASP 3.1 1.6 + - - -
62A SER* 1.3 79.3 - - - +
64A PHE* 1.3 53.8 + - - +
65A ARG* 2.7 35.5 + - - +
67A ASP* 4.5 0.5 - - - +
68A ARG* 4.1 22.9 + - - +
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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