Contacts of the helix formed by residues 73 - 92 (chain A) in PDB entry 2B5F
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 GLY 73 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A HIS* 3.7 15.6 - - - -
71A SER* 2.6 13.8 + - - -
72A VAL* 1.3 79.1 - - - +
74A LEU* 1.3 60.2 + - - -
75A LEU* 3.0 5.4 - - - -
76A GLY* 2.6 21.5 + - - -
77A ILE 3.1 8.0 + - - -
70B GLY* 6.3 0.4 - - - -
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Residues in contact with LEU 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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62A HIS* 3.9 18.4 + - + +
73A GLY* 1.3 71.0 - - - -
75A LEU* 1.3 55.7 + - - +
77A ILE* 2.6 51.3 + - + +
78A ALA* 2.8 13.9 + - - +
214A ILE* 3.4 37.3 - - + +
215A PRO* 5.5 6.1 - - + -
70B GLY* 2.7 36.3 + - - +
71B SER* 5.1 2.4 + - - -
72B VAL* 4.5 14.1 - - + +
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Residues in contact with LEU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A VAL 5.0 1.3 - - - +
73A GLY* 4.6 2.7 - - - -
74A LEU* 1.3 77.6 - - - +
76A GLY* 1.3 61.8 + - - +
78A ALA* 3.3 2.2 + - - +
79A TRP* 3.1 25.8 + - + +
207A PHE* 3.9 17.7 - - + -
211A LEU* 3.9 22.7 - - + -
72B VAL* 3.4 28.7 + - - +
75B LEU* 3.4 44.0 - - + -
76B GLY* 4.1 11.0 - - - +
79B TRP* 4.4 4.9 - - + -
75C LEU* 3.7 20.2 - - + -
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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
----------------------------------------------------------
58A THR* 4.4 1.0 - - - +
72A VAL* 3.4 27.1 + - - -
73A GLY 2.6 17.7 + - - -
75A LEU* 1.3 75.0 - - - +
77A ILE* 1.3 59.1 + - - -
79A TRP* 3.3 9.1 + - - +
80A ALA* 3.0 21.7 + - - +
75C LEU* 4.4 10.7 - - - +
211C LEU* 4.0 6.3 - - - +
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Residues in contact with ILE 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A THR* 3.9 25.1 - - + +
59A VAL* 3.6 42.8 - - + +
62A HIS* 4.1 16.6 - - + -
63A SER* 5.7 1.3 - - - +
72A VAL* 4.9 0.4 - - + -
73A GLY 3.1 7.2 + - - +
74A LEU* 2.6 41.5 + - + +
76A GLY* 1.3 71.3 - - - +
78A ALA* 1.3 62.6 + - - +
80A ALA* 3.1 11.1 + - + +
81A PHE* 3.2 32.1 + - + -
214A ILE* 4.2 14.6 - - + -
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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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74A LEU 2.8 13.2 + - - +
75A LEU 3.5 8.3 - - - +
77A ILE* 1.3 73.8 - - - +
79A TRP* 1.3 57.4 + - - +
81A PHE* 3.4 3.3 + - - +
82A GLY 3.1 23.0 + - - -
207A PHE* 3.6 26.2 - - + -
210A HIS* 3.8 25.7 - - + +
211A LEU* 3.8 20.4 - - + +
214A ILE* 4.2 6.7 - - + +
72B VAL* 5.3 0.2 - - + -
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Residues in contact with TRP 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 LEU* 3.1 32.1 + - + +
76A GLY* 3.5 9.4 - - - +
77A ILE 3.2 0.2 - - - -
78A ALA* 1.3 74.3 - - - +
80A ALA* 1.3 61.0 + - - +
82A GLY 4.5 0.2 - - - +
83A GLY* 2.8 34.6 + - - -
203A GLY 6.4 0.9 - - - -
204A PHE* 3.9 24.7 - + - -
207A PHE* 3.3 48.2 - + + -
79B TRP* 3.6 31.8 - + - +
75C LEU* 4.5 10.2 - - + +
79C TRP* 4.0 24.6 - + - +
204C PHE* 4.0 30.5 - + - -
207C PHE* 4.3 17.5 - + + -
208C MET* 3.6 5.4 - - - +
211C LEU* 4.2 11.7 - - + -
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Residues in contact with ALA 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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54A ILE* 4.8 5.4 - - + -
55A THR* 3.6 22.1 - - + +
58A THR* 4.0 23.8 - - + +
76A GLY 3.0 12.5 + - - +
77A ILE* 3.1 8.9 + - - +
79A TRP* 1.3 73.9 - - - +
81A PHE* 1.3 62.0 + - + +
84A MET* 3.1 31.6 + - - +
208C MET* 4.0 9.9 - - - -
211C LEU* 4.1 6.9 - - + +
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Residues in contact with PHE 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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51A PHE* 3.8 17.8 - + - -
55A THR* 3.4 36.6 - - + -
56A VAL* 4.9 2.5 - - + -
59A VAL* 3.8 11.2 - - + -
77A ILE* 3.2 39.9 + - + -
78A ALA 3.8 4.3 - - - +
79A TRP 3.2 0.2 - - - -
80A ALA* 1.3 80.5 - - + +
82A GLY* 1.3 62.8 + - - +
85A ILE* 3.3 28.1 + - - +
206A VAL* 3.8 3.4 - - + -
210A HIS* 3.1 42.4 - + + +
218A GLY 5.7 1.3 - - - -
225A ARG* 3.6 48.7 - - + -
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Residues in contact with GLY 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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78A ALA 3.1 13.4 + - - -
79A TRP* 5.4 1.3 - - - -
81A PHE* 1.3 76.8 - - - +
83A GLY* 1.3 57.8 + - - +
85A ILE* 3.3 2.4 + - - +
86A PHE 3.1 22.9 + - - -
203A GLY* 3.1 33.3 - - - -
206A VAL* 3.8 5.5 - - - +
207A PHE* 3.7 15.9 - - - -
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Residues in contact with GLY 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 TRP* 2.8 26.8 + - - +
82A GLY* 1.3 70.0 - - - +
84A MET* 1.3 58.5 + - - +
86A PHE* 3.5 7.0 + - - +
87A VAL* 3.0 32.4 + - - +
204C PHE* 4.3 15.4 - - - -
208C MET* 3.6 17.0 - - - -
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Residues in contact with MET 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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50A LEU* 3.2 30.5 - - + +
51A PHE* 4.0 17.0 - - + -
54A ILE* 3.5 38.1 - - + -
55A THR* 4.8 2.2 - - + -
80A ALA 3.1 25.2 + - - +
82A GLY 3.3 0.2 - - - -
83A GLY* 1.3 72.9 - - - +
85A ILE* 1.3 62.0 + - - +
87A VAL* 4.4 6.7 - - + -
88A LEU* 2.9 64.1 + - + +
174C VAL* 4.7 14.1 - - + -
208C MET* 3.6 21.9 - - - -
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Residues in contact with ILE 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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51A PHE* 3.2 41.5 - - + -
81A PHE 3.3 9.7 + - - +
82A GLY 3.3 7.4 + - - +
84A MET* 1.3 77.0 - - - +
86A PHE* 1.3 56.4 + - - +
88A LEU* 4.6 1.6 - - + -
89A VAL* 2.9 46.8 + - + +
99A HIS 5.4 1.1 - - - +
100A ILE* 4.1 27.8 - - + +
101A ASN* 6.1 1.3 - - + -
202A ILE* 3.1 35.2 - - + -
206A VAL* 4.0 17.0 - - + -
222A ASN* 5.2 2.2 - - - +
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Residues in contact with PHE 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 GLY 3.1 7.7 + - - +
83A GLY* 3.5 7.4 - - - +
85A ILE* 1.3 76.8 - - - +
87A VAL* 1.3 64.5 + - + +
90A TYR* 3.0 30.6 + + + +
196A ILE* 6.4 3.6 - - + -
199A PRO* 3.1 53.8 - - + +
200A LEU* 3.4 28.3 - - + -
203A GLY* 3.5 19.0 - - - -
200C LEU* 3.7 26.2 - - + -
201C PRO* 3.6 28.5 - - + -
204C PHE* 3.9 33.4 - + + -
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Residues in contact with VAL 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 GLY 3.0 19.2 + - - +
84A MET* 3.8 9.6 - - - +
86A PHE* 1.3 76.9 - - + +
88A LEU* 1.3 67.6 + - + +
90A TYR* 3.3 8.8 + - - +
91A CYS* 2.9 32.6 + - - -
174C VAL* 5.1 9.4 - - + -
178C THR* 3.8 26.9 - - + +
201C PRO* 4.2 4.9 - - - +
204C PHE* 4.0 27.1 - - + -
205C ALA* 4.1 13.9 - - + +
208C MET* 4.4 5.8 - - + -
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Residues in contact with LEU 88 (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 ALA* 3.4 38.4 - - + +
50A LEU* 4.8 8.1 - - + -
51A PHE* 3.5 26.7 - - + -
84A MET* 2.9 46.0 + - + +
85A ILE* 4.2 2.9 - - - +
87A VAL* 1.3 80.6 - - + +
89A VAL* 1.3 53.6 + - - +
91A CYS* 3.2 4.5 + - + +
92A THR* 2.6 40.7 + - + +
100A ILE* 4.0 18.2 - - + -
174C VAL* 6.4 0.7 - - + -
177C TYR* 5.0 16.6 - - + -
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Residues in contact with VAL 89 (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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85A ILE* 2.9 41.6 + - + +
86A PHE* 4.3 1.6 - - - +
88A LEU* 1.3 72.2 - - - +
90A TYR* 1.3 63.8 + - - +
92A THR* 3.5 6.1 - - - -
93A ALA* 3.0 31.6 + - + +
97A GLY 4.7 4.5 - - - +
98A GLY* 3.4 27.4 - - - +
99A HIS 5.2 0.9 - - - +
100A ILE* 4.3 9.4 - - + -
198A ALA* 4.6 18.8 - - + +
199A PRO* 4.5 9.2 - - + -
202A ILE* 4.6 14.8 - - + -
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Residues in contact with TYR 90 (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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86A PHE* 3.0 26.4 + + + +
87A VAL* 3.3 7.0 - - - +
89A VAL* 1.3 77.1 - - - +
91A CYS* 1.3 72.8 + - - +
93A ALA* 3.8 11.3 - - - +
192A SER* 4.3 25.5 + - - +
193A HIS* 5.7 1.2 - - - -
196A ILE* 4.0 28.5 - - + +
199A PRO* 3.8 24.2 - - + +
178C THR* 4.9 3.8 - - + -
181C SER* 3.4 34.2 + - - -
182C ALA* 4.0 9.2 - - - -
183C THR 5.5 0.3 + - - -
198C ALA* 4.3 13.1 - - + +
201C PRO* 3.9 36.6 - - + -
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Residues in contact with CYS 91 (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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87A VAL* 2.9 25.9 + - - +
88A LEU* 3.2 6.9 + - + +
90A TYR* 1.3 82.6 - - - +
92A THR* 1.3 67.6 + - + +
95A ILE* 3.9 10.9 - - - +
192A SER* 4.5 3.8 + - - -
177C TYR* 3.6 39.2 + - + +
178C THR* 4.1 27.1 - - - -
181C SER* 4.0 25.7 + - - +
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Residues in contact with THR 92 (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 ALA* 4.0 27.6 - - + +
44A GLU* 4.7 3.1 - - - +
47A ALA* 4.4 11.7 - - + -
88A LEU 2.6 23.2 + - - +
89A VAL* 3.5 1.4 + - - -
91A CYS* 1.3 83.6 - - + +
93A ALA* 1.3 74.1 + - - +
94A GLY 2.7 5.4 + - - -
95A ILE* 2.8 20.3 + - + +
96A SER* 3.7 22.0 - - - +
98A GLY* 3.1 18.8 - - - -
100A ILE* 4.1 2.6 - - + +
192A SER* 4.1 2.3 + - - -
177C TYR* 4.4 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