Contacts of the helix formed by residues 74 - 87 (chain A) in PDB entry 6O81
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 ALA 74 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66A VAL 3.8 11.9 - - - +
67A LEU* 3.9 17.0 - - - +
68A LEU 3.3 10.1 - - - -
69A PRO* 4.3 0.8 - - - +
72A ASN 4.4 0.2 - - - -
73A VAL* 1.3 80.4 - - - +
75A LEU* 1.3 64.4 + - - +
76A ILE 3.2 2.2 - - - +
77A ASP* 3.2 15.9 + - - +
78A TYR* 3.3 11.5 + - - -
105A HIS* 3.5 33.1 - - + +
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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
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65A ARG 4.3 10.5 - - - +
66A VAL 3.5 8.0 + - - +
68A LEU* 3.2 30.7 + - + +
70A LEU* 3.8 24.7 - - + +
74A ALA* 1.3 71.9 - - - +
76A ILE* 1.3 56.6 + - - +
78A TYR* 3.6 8.5 - - - +
79A THR* 2.7 38.9 + - - -
153A GLY 3.9 11.7 - - - +
154A ASP* 3.7 27.8 - - + +
156A ILE* 3.7 24.7 - - + -
300A VAL* 3.8 25.8 - - + -
306A TYR* 5.0 4.9 - - + -
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Residues in contact with ILE 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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47A LEU* 3.8 27.4 - - + -
49A ALA* 3.9 16.2 - - + -
66A VAL* 3.2 28.8 + - + +
67A LEU* 4.4 6.5 - - + -
74A ALA 3.2 0.2 - - - -
75A LEU* 1.3 77.3 - - - +
77A ASP* 1.3 63.8 + - - +
79A THR* 3.4 3.2 + - - +
80A LEU* 2.9 47.5 + - + +
93A VAL* 5.1 2.2 - - + -
102A ILE* 4.6 5.2 - - + -
105A HIS* 4.5 11.4 - - + +
106A LEU* 4.5 21.3 - - + -
153A GLY 3.7 15.0 - - - +
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Residues in contact with ASP 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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73A VAL* 3.8 14.5 - - + +
74A ALA 3.2 16.2 + - - +
76A ILE* 1.3 81.1 - - - +
78A TYR* 1.3 58.1 + - - +
80A LEU* 4.5 0.4 - - - +
81A GLU* 2.9 31.4 + - - +
105A HIS* 3.6 30.0 + - - -
106A LEU* 5.5 0.3 - - - +
109A SER* 4.1 9.9 - - - -
111A TRP* 3.3 36.7 - - + -
327A PHE* 4.0 5.1 - - + -
328A THR* 5.1 7.8 + - - +
333A GLN* 5.8 1.7 + - - -
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Residues in contact with TYR 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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70A LEU* 3.7 23.6 - - + -
71A ALA* 4.2 15.8 + - - +
73A VAL* 3.4 31.1 - - + +
74A ALA 3.3 21.5 + - - -
75A LEU* 3.6 7.9 - - - +
76A ILE 3.3 0.4 - - - -
77A ASP* 1.3 78.8 - - - +
79A THR* 1.3 57.3 + - - +
81A GLU 3.4 0.7 + - - -
82A PHE* 2.9 28.2 + - - +
155A VAL 4.5 2.0 - - - +
156A ILE* 3.7 24.5 - - + -
157A SER 5.5 0.2 + - - -
313A VAL* 3.5 33.3 - - + +
321A LEU* 3.6 36.0 - - + +
322A THR 6.1 0.2 - - - -
323A PRO* 4.6 5.9 - - - +
327A PHE* 3.5 26.9 - + - -
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Residues in contact with THR 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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47A LEU* 3.8 18.2 - - + -
75A LEU 2.7 22.6 + - - -
76A ILE* 3.9 3.8 - - - -
78A TYR* 1.3 75.1 - - - +
80A LEU* 1.3 58.7 + - - +
82A PHE* 3.3 8.5 + - + +
83A LEU* 2.9 29.1 + - + +
151A VAL* 3.8 17.5 - - + -
152A TYR 3.5 22.0 - - - +
153A GLY 3.7 7.1 + - - -
155A VAL* 2.9 31.6 + - + +
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Residues in contact with LEU 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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47A LEU* 4.1 20.9 - - + -
76A ILE* 2.9 37.8 + - + +
77A ASP* 5.1 0.2 - - - +
79A THR* 1.3 72.8 - - - +
81A GLU* 1.3 60.3 + - - +
83A LEU* 3.2 12.7 + - + +
84A THR* 2.9 33.3 + - - +
91A THR* 4.4 9.2 - - + +
93A VAL* 5.1 7.0 - - + -
106A LEU* 5.2 9.9 - - + -
109A SER* 5.2 1.8 - - - +
111A TRP* 3.5 46.4 - - + +
118A ASN* 4.8 2.0 - - - +
120A VAL* 4.4 21.1 - - + -
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Residues in contact with GLU 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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77A ASP 2.9 19.1 + - - +
78A TYR 3.7 3.8 - - - +
80A LEU* 1.3 72.5 - - - +
82A PHE* 1.3 59.3 + - - +
84A THR* 3.1 14.4 + - - -
85A ALA* 2.9 29.2 + - - +
110A LYS* 3.3 26.3 + - - -
111A TRP* 3.5 9.9 - - + -
321A LEU* 3.9 18.9 - - + +
327A PHE* 3.5 40.8 - - + +
20D GLU* 5.9 0.9 - - - +
24D ARG* 4.0 21.3 + - - +
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Residues in contact with PHE 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 TYR 2.9 16.3 + - - +
79A THR* 3.5 17.9 - - + +
81A GLU* 1.3 78.3 - - - +
83A LEU* 1.3 64.9 + - + +
85A ALA* 3.4 6.5 + - + +
86A THR* 2.5 47.9 + - - -
149A LEU* 5.1 0.4 - - + -
151A VAL* 4.7 4.9 - - + -
155A VAL* 5.3 2.2 - - + +
157A SER* 3.3 50.5 - - - +
158A ASN* 3.9 3.1 - - - +
159A ILE* 3.2 29.6 - - + -
161A ILE* 5.0 7.4 - - + -
249A ILE* 3.6 44.2 - - + -
321A LEU* 4.4 3.9 - - + +
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Residues in contact with LEU 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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45A ALA* 4.2 5.8 - - + -
47A LEU* 3.8 29.2 - - + -
79A THR 2.9 16.6 + - - +
80A LEU* 3.2 10.5 + - + +
82A PHE* 1.3 87.8 - - + +
84A THR* 1.3 57.7 + - - +
86A THR* 3.2 5.2 + - - +
87A GLY 3.1 21.8 + - - -
88A VAL* 3.3 37.1 - - + +
91A THR* 3.8 23.6 - - + -
118A ASN* 4.3 3.1 - - - +
149A LEU* 3.8 31.9 - - + -
151A VAL* 4.3 9.0 - - + -
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Residues in contact with THR 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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80A LEU 2.9 14.8 + - - +
81A GLU* 3.1 25.1 + - - -
83A LEU* 1.3 75.1 - - - +
85A ALA* 1.3 57.7 + - - +
87A GLY* 3.6 10.8 + - - +
88A VAL* 5.0 2.2 - - - +
110A LYS* 5.6 0.7 + - - -
111A TRP* 3.4 24.9 + - + +
116A SER* 5.6 0.4 - - - +
117A LEU* 4.5 10.8 - - + +
118A ASN* 3.6 27.6 - - + +
24D ARG* 2.7 43.6 + - - -
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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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81A GLU* 2.9 20.3 + - - +
82A PHE* 3.8 9.4 - - + +
84A THR* 1.3 74.3 + - - +
86A THR* 1.3 65.0 + - - +
158A ASN* 6.0 5.8 - - - +
159A ILE 5.6 1.6 - - - -
160A ASN* 4.2 10.7 - - - +
320A PRO* 6.4 2.9 - - + -
321A LEU* 5.1 9.4 - - + -
24D ARG* 4.0 27.4 + - + +
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Residues in contact with THR 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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43A LEU* 4.7 9.7 - - + +
82A PHE* 2.5 42.4 + - - -
83A LEU* 3.2 11.5 + - - -
85A ALA* 1.3 78.9 - - - +
87A GLY* 1.3 57.6 + - - +
88A VAL* 4.6 7.6 - - + -
149A LEU* 4.5 9.2 - - + -
159A ILE 4.0 4.0 + - - +
160A ASN* 3.5 15.4 - - - +
161A ILE* 3.7 39.5 - - + +
162A THR* 4.3 10.9 - - + +
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Residues in contact with GLY 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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43A LEU* 4.1 14.0 - - - +
83A LEU 3.1 3.0 + - - -
84A THR 3.6 9.3 + - - -
85A ALA 3.5 1.6 - - - -
86A THR* 1.3 79.1 - - - +
88A VAL* 1.3 65.3 + - - +
89A GLN* 3.1 18.6 - - - +
117A LEU* 6.4 1.1 - - - -
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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