Contacts of the helix formed by residues 41 - 59 (chain A) in PDB entry 1BO1
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 41 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A SER 3.8 6.5 - - - +
40A GLU* 1.3 83.7 - - + +
42A ILE* 1.3 64.9 + - + +
44A SER* 3.2 9.8 + - - +
45A VAL* 3.0 34.2 + - - +
88A ASN 5.2 2.5 - - - +
90A PRO* 3.8 22.4 - - + +
191A VAL* 4.3 12.1 - - + -
192A ASP* 6.1 0.4 - - - +
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Residues in contact with ILE 42 (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 GLU* 3.0 36.3 - - + +
41A PRO* 1.3 87.2 - - + +
43A LEU* 1.3 60.7 + - + +
45A VAL* 3.4 0.8 + - - -
46A LEU* 3.1 22.7 + - - +
138A ARG* 4.5 8.1 - - - +
189A LEU* 3.4 19.9 - - + +
191A VAL* 4.5 20.0 - - + -
196A THR* 4.4 20.9 - - + +
198A MET* 4.4 17.4 - - + +
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Residues in contact with LEU 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ALA* 3.5 24.0 - - + -
39A SER* 4.9 6.1 - - - +
40A GLU* 3.0 30.0 + - + +
42A ILE* 1.3 83.2 - - + +
44A SER* 1.3 57.0 + - - +
46A LEU* 3.6 10.5 + - + +
47A MET* 3.0 35.9 + - - +
125A ALA* 5.1 1.3 - - + -
126A PRO* 3.5 35.1 - - + +
128A ASN* 5.2 3.8 - - - +
138A ARG* 5.5 3.6 - - - +
140A LEU* 3.5 29.4 - - + -
198A MET* 5.0 7.2 - - + -
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Residues in contact with SER 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 2.9 34.8 - - - +
38A ALA* 3.0 16.2 + - - +
39A SER 5.1 0.2 + - - -
40A GLU 3.4 5.3 + - - -
41A PRO* 3.2 11.0 + - - +
42A ILE 3.2 0.6 - - - -
43A LEU* 1.3 74.5 - - - +
45A VAL* 1.3 61.6 + - - +
46A LEU 3.2 0.4 - - - -
47A MET 3.6 0.3 + - - -
48A TRP* 3.0 29.1 + - - +
88A ASN 3.1 23.6 + - - -
89A LEU* 3.4 10.5 - - - +
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Residues in contact with VAL 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PRO 3.0 19.9 + - - +
42A ILE 3.4 1.1 + - - +
44A SER* 1.3 73.5 - - - +
46A LEU* 1.3 58.7 + - - +
48A TRP* 3.7 6.5 - - - +
49A GLY* 2.8 24.8 + - - -
89A LEU* 4.6 0.2 - - - -
90A PRO* 3.6 19.5 - - + -
93A PHE* 3.6 46.4 - - + -
94A LYS 4.0 15.3 - - - +
95A PHE* 3.7 7.6 - - + -
189A LEU* 3.5 21.1 - - + -
191A VAL* 4.0 9.4 - - + -
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Residues in contact with LEU 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A ILE 3.1 17.2 + - - +
43A LEU* 3.7 11.7 - - + +
45A VAL* 1.3 74.3 - - - +
47A MET* 1.3 61.2 + - + +
49A GLY* 2.8 4.0 + - - -
50A VAL* 2.8 47.6 + - + +
95A PHE* 4.2 11.0 - - + -
121A VAL* 4.2 8.1 - - + -
126A PRO* 4.6 11.7 - - + -
140A LEU* 5.0 0.7 - - + -
149A ILE* 3.5 33.9 - - + -
187A TYR* 4.5 11.7 - - + -
189A LEU* 3.2 9.6 - - + +
198A MET* 3.9 28.5 - - + -
200A VAL* 5.4 1.3 - - + -
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Residues in contact with MET 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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36A PHE 4.0 14.8 - - - +
37A ARG* 3.2 17.4 + - - +
38A ALA* 4.0 13.2 - - - -
43A LEU 3.0 19.4 + - - +
44A SER 4.0 2.7 - - - +
46A LEU* 1.3 76.3 - - + +
48A TRP* 1.3 62.5 + - - +
51A ASN* 3.1 24.4 + - - +
121A VAL* 3.2 25.6 - - + +
122A THR* 3.1 37.5 - - + +
123A ARG 4.8 0.2 - - - -
124A SER* 3.9 1.1 - - - -
125A ALA* 3.6 42.2 - - + +
126A PRO* 4.0 8.5 - - + -
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Residues in contact with TRP 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A ARG* 3.2 16.8 - - - +
44A SER 3.0 19.3 + - - +
45A VAL* 3.7 6.3 - - - +
47A MET* 1.3 76.6 - - - +
49A GLY* 1.3 65.5 + - - +
51A ASN* 3.7 3.0 - - - +
52A HIS* 2.9 50.5 + + + +
77A ILE* 3.8 26.7 - - + -
79A VAL* 3.7 18.5 - - + +
89A LEU* 3.3 35.3 - - + +
93A PHE* 3.8 22.1 - + - -
95A PHE* 4.1 18.4 - - + -
52B HIS* 4.3 20.4 - + - -
56B GLU* 2.9 26.2 + - - -
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Residues in contact with GLY 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 VAL 2.8 8.5 + - - -
46A LEU 2.8 7.9 + - - -
48A TRP* 1.3 82.5 - - - +
50A VAL* 1.3 55.6 + - - -
51A ASN 3.0 4.7 - - - -
53A THR* 2.8 36.4 + - - +
95A PHE* 3.3 31.6 - - - -
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Residues in contact with VAL 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 LEU* 2.8 35.9 + - + +
47A MET 4.5 0.9 - - - +
49A GLY* 1.3 72.1 - - - -
51A ASN* 1.3 57.6 + - - +
53A THR* 3.5 7.9 - - - -
54A ILE* 3.1 42.0 + - + +
95A PHE* 3.9 0.6 - - + -
117A TYR* 3.8 16.8 - - + +
118A GLN* 4.2 9.8 + - - +
121A VAL* 3.8 31.6 - - + -
122A THR* 4.7 0.4 - - + -
187A TYR* 3.6 27.1 - - + +
200A VAL* 5.3 0.9 - - + -
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Residues in contact with ASN 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A LEU* 3.6 28.0 - - - +
37A ARG* 4.4 6.0 + - - +
47A MET 3.1 20.6 + - - +
48A TRP* 3.7 6.0 - - - +
49A GLY 3.0 0.6 - - - -
50A VAL* 1.3 77.5 - - - +
52A HIS* 1.3 61.6 + - - +
55A ASN* 3.0 43.4 + - - +
118A GLN* 3.0 33.7 + - - +
122A THR* 3.5 12.5 + - + +
59B ASN* 4.8 9.7 + - - -
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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
----------------------------------------------------------
48A TRP* 2.9 37.8 + + + +
49A GLY 3.3 3.1 + - - +
51A ASN* 1.3 80.2 + - - +
53A THR* 1.3 56.4 + - + +
55A ASN* 3.8 4.6 - - - +
56A GLU* 2.8 67.1 + - + +
77A ILE* 3.7 40.5 - - + +
48B TRP* 4.2 11.7 - + - -
52B HIS* 3.6 35.4 + + - -
56B GLU* 5.2 0.8 + - - +
79B VAL* 5.9 0.4 - - - +
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Residues in contact with THR 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 GLY 2.8 28.3 + - - +
50A VAL* 3.5 10.7 + - - -
52A HIS* 1.3 77.5 - - + +
54A ILE* 1.3 65.4 + - - +
56A GLU* 3.5 7.3 + - - +
57A LEU* 2.9 33.7 + - - +
75A SER* 4.4 6.7 - - - +
77A ILE* 4.6 1.8 - - + -
95A PHE* 3.6 24.9 - - + -
97A GLU* 3.3 35.5 + - + +
187A TYR* 4.1 8.1 - - - -
84B PHE* 5.9 0.2 - - - -
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Residues in contact with ILE 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 VAL* 3.1 24.7 + - + +
52A HIS 3.4 0.4 - - - -
53A THR* 1.3 83.8 + - - +
55A ASN* 1.3 67.2 + - - +
57A LEU* 3.1 8.2 + - + +
58A SER* 3.0 20.0 + - - -
97A GLU* 5.6 0.9 - - - +
107A ARG* 3.8 12.3 - - - +
114A ASP* 3.9 35.6 - - + +
115A GLN* 5.2 0.2 - - - -
117A TYR* 3.3 37.5 - - + -
118A GLN* 3.1 39.0 - - + +
187A TYR* 4.4 2.5 - - - +
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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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51A ASN* 3.0 37.0 + - - +
52A HIS* 3.8 4.2 - - - +
54A ILE* 1.3 75.1 - - - +
56A GLU* 1.3 58.4 + - - +
58A SER* 2.7 40.3 + - - +
59A ASN* 3.7 6.9 + - - -
118A GLN* 3.0 24.1 + - - +
55B ASN* 6.2 0.2 - - - +
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Residues in contact with GLU 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 HIS* 2.8 50.3 + - + +
53A THR* 3.5 9.6 - - - +
55A ASN* 1.3 78.1 - - - +
57A LEU* 1.3 60.3 + - - +
59A ASN* 3.3 19.6 + - - +
60A VAL* 3.3 14.5 + - - +
37B ARG* 5.8 0.9 + - - -
48B TRP* 2.8 35.0 + - - -
52B HIS* 5.2 0.5 + - - -
81B ASN* 6.1 0.7 - - - +
84B PHE* 4.9 11.0 - - + -
85B ASN* 4.1 19.1 - - - +
89B LEU* 4.8 0.5 - - - +
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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 THR 2.9 20.8 + - - +
54A ILE* 3.5 7.9 - - + +
55A ASN 3.1 0.4 - - - -
56A GLU* 1.3 73.8 - - - +
58A SER* 1.3 56.8 + - - +
59A ASN 3.0 10.2 + - - -
60A VAL* 3.1 38.5 + - + +
97A GLU* 4.3 10.3 - - - +
100A PRO* 3.9 11.2 - - + +
101A MET* 4.1 6.1 - - - -
104A ARG* 3.1 58.6 + - + +
107A ARG* 3.8 20.9 - - - +
114A ASP* 4.3 5.2 - - - +
84B PHE* 4.0 20.9 - - + -
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Residues in contact with SER 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A ILE 3.0 10.2 + - - -
55A ASN* 2.7 28.9 + - - +
57A LEU* 1.3 70.3 - - - +
59A ASN* 1.3 69.9 + - - +
60A VAL 5.0 0.7 - - - -
104A ARG* 5.1 1.8 - - - +
114A ASP* 5.8 0.2 + - - -
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Residues in contact with ASN 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 ASN 3.9 12.7 + - - -
56A GLU* 3.3 14.6 + - - +
57A LEU 3.0 1.0 - - - -
58A SER* 1.3 88.7 + - - +
60A VAL* 1.3 58.5 + - - +
61A PRO* 3.2 11.7 - - - +
36B PHE* 4.3 20.4 + - - +
37B ARG* 4.0 24.1 - - - +
51B ASN* 5.0 8.7 + - - -
85B ASN* 5.9 2.2 - - - +
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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
------------------------------------------------------------
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