Contacts of the helix formed by residues 75 - 97 (chain A) in PDB entry 1I60
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 ASP 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A ARG* 1.3 77.3 + - - +
76A GLU* 1.3 66.5 + - - +
77A LYS* 3.4 16.2 + - - +
78A GLY* 2.9 26.3 + - - -
79A HIS* 2.8 21.6 + - - +
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A ASP* 1.3 75.7 - - - +
77A LYS* 1.3 62.1 + - - +
79A HIS* 3.6 15.3 + - - +
80A ASN* 3.1 22.2 + - - +
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Residues in contact with LYS 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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74A ARG* 5.7 2.5 - - - +
75A ASP* 3.2 15.4 + - - +
76A GLU* 1.3 77.3 - - - +
78A GLY* 1.3 69.3 + - - +
80A ASN* 3.1 10.2 + - + +
81A GLU* 3.1 43.7 + - + +
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Residues in contact with GLY 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 ARG* 3.4 35.1 + - - -
75A ASP* 2.9 16.7 + - - -
77A LYS* 1.3 75.4 - - - +
79A HIS* 1.3 64.6 + - - +
81A GLU* 3.1 9.7 + - - +
82A ILE* 3.0 27.7 + - - +
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Residues in contact with HIS 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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71A PHE 5.8 2.0 - - - -
74A ARG* 3.8 11.1 - - + +
75A ASP 2.8 18.6 + - - +
76A GLU* 3.7 16.2 + - - +
78A GLY* 1.3 75.4 - - - +
80A ASN* 1.3 61.5 + - - +
82A ILE* 3.2 8.1 + - + +
83A ILE* 2.9 53.3 + - + +
124A VAL* 4.6 20.9 - - + -
127A GLU* 2.8 30.8 + - - -
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Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLU* 3.1 14.2 + - - +
77A LYS* 3.1 13.1 + - - +
79A HIS* 1.3 83.1 + - - +
81A GLU* 1.3 60.1 + - - +
83A ILE* 4.2 3.5 - - - +
84A THR* 2.6 48.3 + - - -
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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
----------------------------------------------------------
74A ARG* 3.6 19.8 + - - +
77A LYS* 3.1 43.4 + - + +
78A GLY* 3.1 9.8 + - - +
80A ASN* 1.3 80.1 - - - +
82A ILE* 1.3 61.4 + - + +
84A THR* 3.8 3.9 - - - -
85A GLU* 3.0 32.1 + - - +
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Residues in contact with ILE 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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68A LEU* 3.5 32.6 - - + +
69A VAL 3.4 18.8 - - - +
70A PHE 3.3 26.2 - - - +
71A PHE* 3.7 24.9 - - + +
74A ARG* 3.8 9.0 - - + +
78A GLY 3.0 18.4 + - - +
79A HIS* 3.2 11.2 + - + +
81A GLU* 1.3 78.4 - - + +
83A ILE* 1.3 61.0 + - + +
85A GLU* 4.9 3.6 - - - +
86A PHE* 3.0 27.5 + - - +
124A VAL* 4.6 10.1 - - + -
128A LEU* 4.7 4.0 - - + -
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Residues in contact with ILE 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 HIS* 2.9 44.8 + - + +
80A ASN* 4.2 3.4 - - - +
82A ILE* 1.3 76.3 - - + +
84A THR* 1.3 66.5 + - - +
86A PHE* 3.3 3.8 + - - +
87A LYS* 3.0 51.9 + - + +
124A VAL* 5.1 2.7 - - + -
127A GLU* 3.6 31.9 - - + +
128A LEU* 3.8 25.8 - - + -
131A ILE* 4.0 8.1 - - + -
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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 ASN* 2.6 38.9 + - - -
81A GLU* 3.8 5.2 - - - -
83A ILE* 1.3 79.0 - - - +
85A GLU* 1.3 63.9 + - - +
87A LYS* 3.3 8.6 + - - +
88A GLY* 3.1 17.8 + - - -
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Residues in contact with GLU 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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35A THR* 4.4 14.9 + - - +
36A MSE 6.2 0.2 - - - -
67A ALA 4.9 3.1 - - - +
68A LEU* 3.9 19.9 - - + +
69A VAL* 4.7 4.5 + - - +
81A GLU 3.0 18.9 + - - +
82A ILE* 4.0 6.2 - - - +
84A THR* 1.3 77.4 - - - +
86A PHE* 1.3 59.1 + - - +
88A GLY* 3.2 3.0 + - - +
89A MSE 2.9 43.2 + - + +
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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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68A LEU* 3.8 24.2 - - + +
82A ILE 3.0 18.0 + - - +
83A ILE* 3.7 4.3 - - + +
85A GLU* 1.3 78.5 - - - +
87A LYS* 1.3 61.6 - - - +
89A MSE 3.1 7.7 + - - +
90A MSE 3.0 59.2 + - + +
101A VAL* 3.7 25.1 - - + -
128A LEU* 3.4 44.4 - - + -
131A ILE* 3.8 19.3 - - + -
132A ALA* 4.1 2.0 - - + -
137A VAL* 5.4 0.2 - - + -
139A ILE* 3.8 30.1 - - + -
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Residues in contact with LYS 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 ILE* 3.0 41.7 + - + +
84A THR* 3.7 7.0 - - - +
86A PHE* 1.3 76.3 - - - +
88A GLY* 1.3 63.5 + - - +
90A MSE 3.3 22.0 + - - +
91A GLU* 3.6 10.0 + - - +
131A ILE* 3.8 29.4 - - + -
135A TYR* 4.8 1.9 + - - -
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Residues in contact with GLY 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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84A THR 3.1 13.6 + - - -
85A GLU* 3.2 4.6 + - - -
87A LYS* 1.3 76.7 - - - +
89A MSE 1.3 62.2 + - - +
91A GLU* 3.2 17.3 + - - +
92A THR* 3.3 14.4 + - - -
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Residues in contact with MSE 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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35A THR* 3.7 24.5 - - + +
65A LEU* 3.5 44.0 - - + +
67A ALA 4.3 9.9 - - - +
68A LEU* 4.3 17.9 - - - -
85A GLU* 2.9 36.5 + - + +
86A PHE* 3.1 10.1 + - - +
88A GLY* 1.3 75.4 - - - +
90A MSE 1.3 68.0 + - + +
92A THR* 3.1 9.4 + - - -
93A CYS* 2.8 32.6 + - - -
101A VAL* 4.0 24.0 - - + -
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Residues in contact with MSE 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 46.0 + - + +
87A LYS* 3.5 9.6 - - - +
88A GLY 3.2 0.4 - - - -
89A MSE 1.3 76.5 - - - +
91A GLU* 1.3 58.3 + - - +
93A CYS* 3.3 5.4 + - - +
94A LYS* 2.9 29.1 + - - +
101A VAL* 3.6 26.7 - - + -
131A ILE* 4.1 15.0 - - + -
132A ALA* 3.8 26.2 - - - -
135A TYR* 3.5 39.4 - - + -
137A VAL* 3.7 22.2 - - + -
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Residues in contact with GLU 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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48A LEU* 5.8 0.7 - - - -
87A LYS 3.6 7.6 + - - +
88A GLY* 3.2 12.4 + - - +
90A MSE 1.3 78.6 - - - +
92A THR* 1.3 62.4 + - - +
94A LYS* 3.3 17.9 + - - +
95A THR* 3.0 30.5 + - - -
135A TYR* 2.6 32.8 + - - +
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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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39A LEU* 4.0 22.9 - - + +
48A LEU* 4.2 22.3 - - + +
65A LEU* 4.1 16.8 - - + -
88A GLY 3.3 12.4 + - - -
89A MSE 3.1 10.2 + - - -
91A GLU* 1.3 79.4 - - - +
93A CYS* 1.3 57.3 + - - +
95A THR* 3.3 1.3 + - - -
96A LEU* 3.0 49.4 + - + +
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Residues in contact with CYS 93 (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 LEU* 3.5 19.7 - - - -
89A MSE 2.8 19.3 + - - +
90A MSE 3.3 6.5 + - - +
92A THR* 1.3 78.0 - - - +
94A LYS* 1.3 53.9 + - - +
97A GLY* 2.7 31.0 + - - -
98A VAL* 2.9 35.4 + - - +
101A VAL* 3.7 21.8 - - - -
137A VAL* 3.7 27.4 - - + -
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Residues in contact with LYS 94 (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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90A MSE 2.9 17.3 + - - +
91A GLU* 3.6 20.0 + - - +
93A CYS* 1.3 79.4 - - - +
95A THR* 1.3 63.2 + - - +
97A GLY* 3.7 5.8 + - - -
135A TYR* 4.2 26.0 - - + +
137A VAL* 5.4 0.4 - - - +
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Residues in contact with THR 95 (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 LEU* 4.1 39.0 - - + +
49A ASP* 4.2 16.8 - - - +
52A ALA* 3.5 16.1 - - + +
91A GLU* 3.0 20.1 + - - +
92A THR 3.3 4.0 + - - -
94A LYS* 1.3 80.8 - - - +
96A LEU* 1.3 60.3 + - + +
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Residues in contact with LEU 96 (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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33A ILE* 4.3 15.3 - - + -
39A LEU* 5.0 4.0 - - + -
48A LEU* 3.5 45.1 - - + +
51A LEU* 3.7 31.2 - - + -
52A ALA* 3.7 20.0 - - + +
55A PHE* 4.3 9.6 - - + +
62A PRO* 3.5 17.8 - - + +
65A LEU* 5.2 0.9 - - + -
92A THR* 3.0 28.3 + - + +
95A THR* 1.3 79.0 - - + +
97A GLY* 1.3 63.2 + - - +
98A VAL* 3.8 14.6 - - + -
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Residues in contact with GLY 97 (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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61A LYS* 6.0 0.2 - - - +
62A PRO* 3.9 11.2 - - - +
93A CYS 2.7 15.5 + - - -
94A LYS 3.7 5.0 + - - -
95A THR 3.5 2.8 + - - -
96A LEU* 1.3 75.4 - - - +
98A VAL* 1.3 60.4 + - - -
99A LYS* 3.7 2.6 + - - +
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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
------------------------------------------------------------
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