Contacts of the helix formed by residues 71 - 87 (chain A) in PDB entry 1BFD
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 SER 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A ASN* 3.7 6.1 - - - -
28A GLU* 3.4 2.2 + - - -
69A LEU 3.7 3.0 + - - -
70A HIS* 1.3 87.6 - - - +
72A ALA* 1.3 62.0 + - - +
73A ALA* 4.7 1.3 - - - -
75A THR* 2.7 31.4 + - - -
96A ALA* 4.0 2.8 - - - +
97A GLY 3.2 26.8 + - - +
110A LEU* 2.7 32.1 + - - -
111A THR 3.9 0.5 + - - -
112A ASN* 3.6 22.6 + - - +
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Residues in contact with ALA 72 (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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71A SER* 1.3 80.7 + - - +
73A ALA* 1.3 54.6 - - - +
75A THR* 3.7 1.0 - - - -
76A GLY* 2.7 34.0 + - - -
111A THR 4.8 4.0 - - - +
112A ASN* 3.6 27.7 - - - +
113A VAL 5.3 0.9 - - - +
118A LEU* 3.8 18.8 - - + +
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Residues in contact with ALA 73 (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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70A HIS* 3.8 8.0 + - + +
71A SER* 3.5 1.0 - - - -
72A ALA* 1.3 78.0 - - - +
74A GLY* 1.3 57.3 + - - +
76A GLY* 3.4 0.8 + - - -
77A ASN* 3.0 38.2 + - - +
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Residues in contact with GLY 74 (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 GLU* 3.2 50.0 - - - +
69A LEU* 3.7 6.8 - - - +
70A HIS* 2.7 30.7 + - - +
73A ALA* 1.3 73.4 - - - +
75A THR* 1.3 62.4 + - - +
77A ASN 3.4 4.9 + - - -
78A ALA 3.4 0.3 + - - -
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Residues in contact with THR 75 (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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69A LEU* 4.0 13.8 - - + +
71A SER 2.7 23.6 + - - -
72A ALA 3.7 2.7 - - - -
74A GLY* 1.3 75.5 - - - +
76A GLY* 1.3 62.9 + - - +
78A ALA* 3.0 15.1 + - - +
79A MET* 3.3 23.0 + - - +
82A LEU* 5.5 3.4 - - + -
94A VAL* 5.6 0.7 - - + -
96A ALA* 3.4 8.1 - - - +
118A LEU* 3.8 19.5 - - + -
119A PRO* 4.7 3.1 - - + -
155A TYR* 2.9 43.5 + - + +
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Residues in contact with GLY 76 (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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72A ALA 2.7 21.6 + - - -
73A ALA* 3.8 1.8 - - - -
75A THR* 1.3 74.9 - - - +
77A ASN* 1.3 61.0 + - - +
78A ALA 3.1 1.0 + - - -
79A MET* 3.2 25.6 + - - +
80A GLY 4.9 0.5 + - - -
118A LEU* 4.5 8.3 - - - +
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Residues in contact with ASN 77 (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 GLN* 3.6 24.0 + - - +
47A GLU* 3.0 33.1 + - + +
48A ALA* 3.7 18.9 + - - +
73A ALA* 3.0 21.9 + - - +
74A GLY 3.7 2.7 - - - +
75A THR 3.3 0.4 - - - -
76A GLY* 1.3 74.9 - - - +
78A ALA* 1.3 57.3 + - - +
79A MET 3.5 0.6 + - - -
80A GLY 4.8 2.4 + - - -
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Residues in contact with ALA 78 (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 GLU* 3.8 10.8 - - + +
48A ALA* 4.3 2.9 - - - +
51A VAL* 3.5 28.0 - - + -
69A LEU* 3.6 18.6 - - + -
74A GLY 3.4 2.2 + - - +
75A THR 3.0 11.4 + - - +
77A ASN* 1.3 78.6 - - - +
79A MET* 1.3 61.3 + - - +
80A GLY 3.3 3.4 - - - -
81A ALA* 3.2 7.9 + - - +
82A LEU* 3.1 26.2 + - + +
94A VAL* 6.1 0.2 - - + -
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Residues in contact with MET 79 (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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75A THR* 3.6 17.9 - - + +
76A GLY* 3.2 20.5 + - - +
77A ASN 3.5 0.2 - - - -
78A ALA* 1.3 74.7 - - - +
80A GLY* 1.3 65.6 + - - +
82A LEU* 3.3 18.9 + - + -
83A SER* 3.2 15.9 + - - -
118A LEU* 4.3 10.5 - - + +
119A PRO* 3.1 48.7 - - + +
120A ARG 5.0 1.8 - - - +
121A PRO* 6.0 0.2 - - + -
122A LEU* 3.4 39.2 - - + +
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Residues in contact with GLY 80 (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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76A GLY 4.9 0.6 + - - -
77A ASN 4.8 2.6 + - - -
78A ALA 3.3 0.8 - - - -
79A MET* 1.3 78.1 - - - +
81A ALA* 1.3 61.2 + - - +
83A SER* 2.6 28.8 + - - -
84A ASN* 3.6 7.7 + - - -
402A GLY* 5.4 2.6 - - - -
530A TPP 6.5 0.9 - - - -
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Residues in contact with ALA 81 (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 ALA* 4.1 23.8 - - + +
51A VAL* 3.7 28.7 - - + +
52A GLY* 4.5 4.7 - - - +
55A ASP* 4.5 3.3 - - - +
78A ALA 3.2 11.3 + - - +
80A GLY* 1.3 76.6 - - - +
82A LEU* 1.3 61.8 + - - +
84A ASN* 3.2 15.0 + - - +
85A ALA* 3.1 19.9 + - - +
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Residues in contact with LEU 82 (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* 4.1 17.7 - - + -
69A LEU* 6.4 0.2 - - + -
75A THR* 5.4 3.8 - - + +
78A ALA* 3.1 21.0 + - + +
79A MET* 3.6 33.9 - - + +
80A GLY 3.2 0.6 - - - -
81A ALA* 1.3 75.0 - - - +
83A SER* 1.3 64.1 + - - +
85A ALA* 3.7 2.3 - - + +
86A TRP* 2.9 24.8 + - - +
92A LEU* 4.5 4.7 - - + -
94A VAL* 4.1 33.2 - - + -
119A PRO* 4.6 4.0 - - + -
122A LEU* 4.2 17.5 - - + +
123A VAL* 4.6 16.6 - - + -
153A PRO* 4.1 18.6 - - + +
155A TYR* 5.9 0.7 - - + -
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Residues in contact with SER 83 (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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79A MET 3.2 5.5 + - - -
80A GLY* 2.6 24.1 + - - -
82A LEU* 1.3 78.2 - - - +
84A ASN* 1.3 64.1 + - - +
86A TRP* 3.4 4.2 + - - +
87A ASN* 3.4 15.4 + - - +
122A LEU* 3.8 27.5 - - - +
400A ALA* 3.4 21.4 - - - +
402A GLY* 5.0 4.9 - - - -
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Residues in contact with ASN 84 (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 ASP* 4.7 1.8 - - - +
80A GLY 4.2 8.2 + - - -
81A ALA* 3.2 12.9 + - - +
83A SER* 1.3 83.0 + - - +
85A ALA* 1.3 62.4 + - - +
87A ASN 3.1 3.1 + - - -
88A SER* 3.0 22.9 + - - -
398A CYS* 3.5 9.8 - - - +
399A ALA* 3.6 11.3 - - + +
400A ALA* 3.0 26.7 + - - +
402A GLY* 2.9 43.0 + - - -
403A LEU 5.2 0.4 + - - -
404A GLY 5.6 0.2 - - - -
405A PHE* 3.7 26.1 - - + +
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Residues in contact with ALA 85 (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 ASP* 3.8 8.9 + - - +
81A ALA 3.1 10.8 + - - +
82A LEU* 3.2 11.9 + - - +
84A ASN* 1.3 79.6 - - - +
86A TRP* 1.3 60.9 + - - +
88A SER* 3.5 8.1 - - - -
89A HIS* 3.1 4.0 + - - -
90A SER* 3.1 30.0 + - - -
92A LEU* 3.6 31.2 - - + -
153A PRO* 3.9 13.4 - - + +
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Residues in contact with TRP 86 (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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82A LEU 2.9 13.4 + - - +
83A SER* 3.5 11.7 - - - +
85A ALA* 1.3 80.1 - - - +
87A ASN* 1.3 76.9 + - - +
89A HIS* 3.3 18.9 + - - -
121A PRO 4.6 9.9 - - - -
122A LEU* 3.6 33.2 - - + +
123A VAL* 3.6 28.7 - - - -
124A LYS* 3.7 18.8 - - + -
152A GLY* 5.5 1.5 - - - -
153A PRO* 4.1 12.4 - - + +
301A ASP* 5.8 2.9 - - - -
303A LEU* 3.9 28.8 - - + +
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Residues in contact with ASN 87 (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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83A SER 3.4 3.2 + - - +
84A ASN 3.1 4.9 + - - +
86A TRP* 1.3 96.7 - - - +
88A SER* 1.3 59.1 + - - +
89A HIS* 3.3 10.0 + - - -
209A PRO* 5.3 4.7 - - - +
238A PRO* 5.1 3.8 - - - +
279A ARG* 3.5 47.6 + - - +
399A ALA* 3.0 40.7 + - + +
400A ALA* 3.5 19.1 - - - +
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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