Contacts of the helix formed by residues 67 - 87 (chain A) in PDB entry 3D87
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 67 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A TRP* 4.8 9.9 - - - -
57A GLY* 4.5 1.6 - - - -
63A LEU* 3.2 34.7 + - - -
66A ASN* 1.3 80.8 + - - +
68A GLN* 1.3 65.8 + - - +
69A PHE* 3.3 3.5 - - - +
70A CYS* 3.7 8.0 - - - +
71A LEU* 2.8 44.9 + - - +
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Residues in contact with GLN 68 (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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4A PRO* 3.5 22.6 - - + +
5A GLY* 3.5 34.3 + - - +
6A GLY 4.3 1.4 - - - +
7A SER* 3.8 24.9 + - - +
66A ASN* 2.7 19.0 - - - +
67A SER* 1.3 78.6 + - - +
69A PHE* 1.3 54.4 + - - +
71A LEU* 3.6 10.6 - - - +
72A GLN* 2.6 56.3 + - - +
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Residues in contact with PHE 69 (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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3A VAL* 5.4 8.1 - - + -
4A PRO* 4.6 27.6 - - + +
55A GLY 4.6 4.0 - - - -
56A ASP* 3.2 45.3 - - + +
57A GLY* 6.0 0.7 - - - -
66A ASN* 4.2 3.5 - - + +
67A SER* 3.3 0.6 - - - -
68A GLN* 1.3 78.8 - - - +
70A CYS* 1.3 62.7 + - - +
72A GLN* 3.1 12.6 + - + +
73A ARG* 2.8 38.5 + - + +
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Residues in contact with CYS 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A ASP 3.1 23.0 + - - +
57A GLY* 3.5 17.0 - - - +
58A CYS* 3.1 32.3 - - - -
63A LEU* 4.1 2.7 - - + -
67A SER* 3.5 9.6 + - - +
68A GLN 3.2 0.2 - - - -
69A PHE* 1.3 78.3 - - - +
71A LEU* 1.3 57.9 + - - +
73A ARG* 2.5 28.8 + - - +
74A ILE* 2.9 30.3 + - - +
160A VAL* 3.6 14.4 - - - -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A SER 4.7 6.7 - - - +
8A SER* 5.7 0.2 - - - -
9A PRO* 3.7 29.4 - - + -
11A TRP* 4.2 13.7 - - + -
67A SER* 2.8 42.1 + - - +
68A GLN* 3.6 12.1 - - - +
70A CYS* 1.3 74.0 - - - +
72A GLN* 1.3 56.9 + - - +
74A ILE* 3.3 10.1 + - + +
75A HIS* 3.0 27.9 + - - +
116A LEU* 4.3 14.2 - - + +
160A VAL* 4.4 10.8 - - + -
161A PHE* 3.5 35.2 - - + -
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Residues in contact with GLN 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PRO* 4.0 20.7 - - - +
68A GLN* 2.6 54.8 + - - +
69A PHE* 3.1 14.3 - - + +
71A LEU* 1.3 74.2 - - - +
73A ARG* 1.3 59.8 + - - +
75A HIS* 3.3 10.6 + - + +
76A GLN* 3.1 18.7 + - - +
117A GLN* 6.2 4.0 - - + -
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Residues in contact with ARG 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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50A PRO* 4.9 2.6 - - - +
51A HIS 3.4 31.9 + - - +
52A ILE* 4.3 12.8 - - + -
53A GLN* 3.7 12.3 - - - +
56A ASP* 2.8 43.2 + - + +
69A PHE* 2.8 27.9 + - + +
70A CYS* 2.5 18.2 + - - +
72A GLN* 1.3 70.0 - - - +
74A ILE* 1.3 61.0 + - - +
76A GLN* 2.8 37.6 + - - +
77A GLY* 2.8 26.0 + - - -
153A PHE* 4.3 2.0 - - + -
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Residues in contact with ILE 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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52A ILE* 3.8 21.8 - - + -
70A CYS* 2.9 46.3 + - - +
71A LEU* 3.4 14.1 - - + +
73A ARG* 1.3 76.2 - - - +
75A HIS* 1.3 59.1 + - - +
77A GLY 3.0 1.6 + - - -
78A LEU* 2.8 40.7 + - + +
116A LEU* 3.5 21.3 - - + -
153A PHE* 3.4 10.5 - - + -
157A ALA* 4.4 13.2 - - + -
160A VAL* 4.1 20.4 - - + -
161A PHE* 4.1 13.7 - - + -
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Residues in contact with HIS 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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71A LEU 3.0 13.4 + - - +
72A GLN* 3.6 13.0 - - + +
73A ARG 3.2 0.2 - - - -
74A ILE* 1.3 75.5 - - - +
76A GLN* 1.3 67.2 + - - +
78A LEU* 3.5 2.9 + - - -
79A ILE* 2.8 62.5 + - + +
113A SER* 3.2 18.1 + - - -
114A GLN* 5.0 0.9 - - - -
116A LEU* 3.9 16.1 - - + +
117A GLN* 2.9 54.3 + - + +
119A GLU* 5.5 0.7 - - - -
120A GLY* 4.8 5.5 + - - -
125A THR* 4.5 12.1 + - + +
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Residues in contact with GLN 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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50A PRO* 4.1 23.3 - - + +
72A GLN 3.1 12.7 + - - +
73A ARG* 2.8 47.5 + - - +
75A HIS* 1.3 82.1 - - - +
77A GLY* 1.3 48.9 + - - +
79A ILE* 3.2 7.2 + - + +
80A PHE* 2.9 32.8 + - + +
127A GLN* 5.5 11.1 - - + +
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Residues in contact with GLY 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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50A PRO* 4.2 15.7 - - - +
73A ARG 2.8 13.3 + - - -
74A ILE 3.0 0.4 + - - -
76A GLN* 1.3 69.6 - - - +
78A LEU* 1.3 55.1 + - - +
80A PHE* 2.9 3.5 + - - +
81A TYR* 2.8 41.4 + - - -
153A PHE* 3.3 29.4 - - - -
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Residues in contact with LEU 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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21A LEU* 4.3 14.8 - - + -
74A ILE* 2.8 27.3 + - + +
75A HIS 3.7 3.1 - - - +
77A GLY* 1.3 68.6 - - - -
79A ILE* 1.3 54.5 + - - +
81A TYR* 4.8 2.9 - - - -
82A GLU* 2.6 39.0 + - - +
109A LEU* 3.7 30.3 - - + +
112A LEU* 3.7 21.8 - - + -
113A SER* 3.3 23.3 - - - +
116A LEU* 3.4 32.3 - - + -
153A PHE* 3.5 18.0 - - + -
154A VAL* 5.0 2.2 - - + -
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Residues in contact with ILE 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 HIS* 2.8 54.9 + - + +
76A GLN* 3.4 7.4 - - + +
78A LEU* 1.3 72.2 - - - +
80A PHE* 1.3 59.1 + - + +
82A GLU* 3.6 9.2 - - + +
83A LYS* 2.9 44.9 + - + +
110A LEU* 5.4 0.9 - - + -
113A SER* 2.8 43.7 - - - +
114A GLN* 5.0 2.7 - - - +
125A THR* 3.8 34.5 - - + +
126A GLN 4.9 2.0 - - - +
127A GLN* 5.5 2.7 - - + -
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Residues in contact with PHE 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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48A ASP* 4.1 17.3 - - + -
49A VAL* 4.0 12.6 - - + -
50A PRO* 3.5 30.7 - - + -
76A GLN 2.9 14.0 + - - +
77A GLY 2.9 5.8 + - - +
79A ILE* 1.3 75.5 - - - +
81A TYR* 1.3 69.2 + - - +
83A LYS* 3.3 6.4 + - + +
84A LEU* 3.1 56.4 + - + +
127A GLN* 3.1 49.4 - - + -
129A PRO* 4.1 16.6 - - + -
130A SER 5.1 2.2 - - - -
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Residues in contact with TYR 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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49A VAL* 3.6 26.2 - - + +
50A PRO* 4.5 5.2 + - + -
77A GLY* 2.8 29.4 + - - +
78A LEU* 4.0 0.9 - - - +
80A PHE* 1.3 71.3 - - + +
82A GLU* 1.3 67.3 + - - +
84A LEU* 2.8 21.8 + - + +
85A LEU* 2.9 14.6 + - + +
109A LEU* 3.4 17.7 - - + -
146A ILE* 3.5 43.1 - - + -
149A SER* 2.7 32.7 + - - -
150A LEU* 3.5 26.7 - - + -
153A PHE* 3.7 36.7 - + + +
181B GLU* 4.4 4.2 + - - -
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Residues in contact with GLU 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 LEU 2.6 24.9 + - - +
79A ILE* 3.6 13.0 - - + +
81A TYR* 1.3 70.5 - - - +
83A LYS* 1.3 70.0 + - + +
85A LEU* 3.3 3.1 + - - +
86A GLY* 3.1 13.5 + - - -
106A HIS* 2.7 39.3 + - - +
109A LEU* 2.9 25.3 - - + +
110A LEU* 3.6 27.7 - - + +
113A SER* 4.4 2.5 - - - +
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Residues in contact with LYS 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 ILE* 2.9 33.2 + - + +
80A PHE* 3.5 8.5 - - - +
82A GLU* 1.3 79.3 - - + +
84A LEU* 1.3 64.7 + - - +
86A GLY* 2.9 13.4 + - - -
87A SER* 2.9 12.3 + - - -
122A HIS* 5.3 7.6 + - - -
125A THR* 3.5 15.5 + - - -
126A GLN* 3.3 32.3 + - - +
127A GLN 4.9 0.4 - - - +
128A ILE* 4.1 11.1 - - + +
129A PRO* 3.6 32.3 - - + -
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Residues in contact with LEU 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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49A VAL* 4.5 3.4 - - + -
80A PHE* 3.1 53.4 + - + +
81A TYR* 2.8 21.3 + - + +
83A LYS* 1.3 74.6 - - - +
85A LEU* 1.3 63.9 + - - +
87A SER* 3.0 27.6 + - - -
89A ILE* 4.2 13.8 - - + +
90A PHE* 3.9 9.2 - - - -
129A PRO* 4.0 16.1 - - + +
130A SER 5.5 1.1 - - - +
142A LEU* 6.0 0.2 - - + -
146A ILE* 3.4 40.2 - - + -
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Residues in contact with LEU 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 TYR 2.9 14.5 + - - +
82A GLU 3.6 8.1 - - - +
84A LEU* 1.3 73.7 - - - +
86A GLY* 1.3 62.0 + - - +
87A SER 3.7 0.2 - - - +
90A PHE* 3.5 58.2 - - + +
91A THR* 4.7 1.7 + - - +
102A VAL* 5.0 3.2 - - + +
105A LEU* 3.0 41.3 - - + -
106A HIS* 3.5 32.0 - - + +
109A LEU* 3.6 17.5 - - + -
146A ILE* 4.5 12.1 - - + -
147A LEU* 4.6 2.5 - - + -
150A LEU* 4.5 6.7 - - + -
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Residues in contact with GLY 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 GLU 3.1 6.4 + - - -
83A LYS* 2.9 9.2 + - - -
85A LEU* 1.3 73.8 - - - +
87A SER* 1.3 69.6 + - - +
91A THR* 3.1 11.1 + - - +
106A HIS* 3.3 20.6 - - - -
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Residues in contact with SER 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 LYS 2.9 10.9 + - - -
84A LEU* 3.0 19.2 + - - -
85A LEU 3.7 1.9 - - - +
86A GLY* 1.3 80.4 - - - +
88A ASP* 1.3 58.7 + - - +
89A ILE* 2.9 35.3 + - - +
90A PHE 3.4 7.1 + - - -
91A THR* 2.5 18.8 + - - -
129A PRO* 5.3 10.3 - - - -
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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