Contacts of the helix formed by residues 78 - 100 (chain A) in PDB entry 1ITF
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 GLU 78 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A SER* 4.5 16.2 - - - +
76A TRP 3.2 5.8 + - - -
77A ASP* 1.3 79.7 - - - +
79A THR* 1.3 77.1 + - - +
81A LEU* 3.7 7.0 - - - +
82A ASP* 2.7 27.4 + - - +
85A TYR* 4.9 2.6 - - - -
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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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77A ASP* 3.0 2.9 - - - -
78A GLU* 1.3 91.5 + - - +
80A LEU* 1.3 70.7 + - + +
81A LEU 3.1 1.1 - - - -
82A ASP* 3.0 19.2 + - + +
83A LYS* 3.0 14.6 + - - +
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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
----------------------------------------------------------
17A LEU* 4.5 10.4 - - + +
20A GLN* 3.1 53.6 - - + +
21A MET* 3.7 24.8 - - + +
23A LYS* 5.1 0.4 - - - -
77A ASP* 3.2 36.4 + - + +
79A THR* 1.3 81.0 - - + +
81A LEU* 1.3 56.9 + - - +
83A LYS* 3.6 5.0 + - + +
84A PHE* 3.0 24.8 + - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 3.3 28.5 - - + -
67A PHE* 3.6 21.1 - - + +
72A SER 3.1 29.2 - - - +
73A SER* 3.4 13.7 - - - +
76A TRP* 3.6 16.4 - - + -
77A ASP 2.7 19.6 + - - +
78A GLU* 4.0 4.7 - - - +
80A LEU* 1.3 70.9 - - - +
82A ASP* 1.3 55.2 + - - +
84A PHE* 2.9 12.4 + - + +
85A TYR* 2.7 67.0 + - + +
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Residues in contact with ASP 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU 2.7 20.7 + - - +
79A THR* 3.0 14.6 + - + +
81A LEU* 1.3 75.6 - - - +
83A LYS* 1.3 62.8 + - - +
85A TYR* 3.0 25.1 + - - +
86A THR* 3.1 17.5 + - - -
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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
----------------------------------------------------------
13A ARG* 5.2 10.1 - - - +
16A MET* 5.2 8.7 - - - +
17A LEU* 3.4 37.0 - - + +
20A GLN* 6.1 0.4 - - - +
79A THR* 3.0 10.9 + - + +
80A LEU* 4.0 5.6 - - + +
82A ASP* 1.3 76.6 - - - +
84A PHE* 1.3 57.1 + - - +
86A THR* 3.2 10.5 + - - -
87A GLU* 2.9 35.6 + - - +
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Residues in contact with PHE 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A THR* 3.2 34.8 - - + -
17A LEU* 3.3 27.6 - - + +
18A LEU* 3.3 21.8 - - + -
21A MET* 3.7 8.5 - - + -
63A ILE* 3.6 16.6 - - + -
67A PHE* 3.5 37.5 - + + -
80A LEU 3.0 16.4 + - - +
81A LEU* 2.9 19.2 + - + +
83A LYS* 1.3 78.9 - - - +
85A TYR* 1.3 54.4 + + - +
88A LEU* 2.9 67.6 + - + +
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Residues in contact with TYR 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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64A PHE* 3.5 36.8 - + + -
67A PHE* 2.7 30.2 + - + -
68A SER* 3.6 31.3 - - - -
73A SER* 3.9 12.3 - - - -
78A GLU* 4.9 2.5 - - - -
81A LEU* 2.7 56.4 + - + +
82A ASP* 3.0 16.1 + - - +
84A PHE* 1.3 74.9 - - - +
86A THR* 1.3 60.1 + - - +
88A LEU* 4.4 3.6 - - + -
89A TYR* 2.9 30.3 + - - +
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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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82A ASP* 3.1 17.3 + - - -
83A LYS* 3.7 13.2 - - - -
85A TYR* 1.3 76.6 - - - +
87A GLU* 1.3 57.3 + - - +
89A TYR* 3.7 5.9 - - + +
90A GLN* 2.8 30.0 + - + +
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Residues in contact with GLU 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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10A GLY* 3.1 30.5 - - - +
13A ARG* 3.2 24.7 - - - +
14A THR* 2.8 37.0 - - - +
17A LEU* 3.3 24.7 - - + -
83A LYS* 2.9 14.2 + - - +
84A PHE 3.9 1.6 - - - +
86A THR* 1.3 76.3 - - - +
88A LEU* 1.3 65.3 + - - +
90A GLN* 3.1 13.0 + - - +
91A GLN* 3.0 27.9 + - - +
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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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14A THR* 3.9 12.1 - - + -
60A ILE* 3.3 29.0 - - + +
63A ILE* 4.0 13.9 - - + +
64A PHE* 3.3 42.8 - - + +
84A PHE* 2.9 70.3 + - + +
85A TYR* 3.3 5.1 + - + +
87A GLU* 1.3 76.8 - - - +
89A TYR* 1.3 55.8 + - - +
91A GLN* 3.6 1.1 + - - -
92A LEU* 2.9 35.3 + - - +
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Residues in contact with TYR 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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64A PHE* 3.5 41.7 - + - -
85A TYR 2.9 14.0 + - - +
86A THR* 3.9 6.3 - - - +
88A LEU* 1.3 75.0 - - - +
90A GLN* 1.3 60.3 + - - +
92A LEU* 3.6 16.4 - - + +
93A ASN* 2.8 33.6 + - + +
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Residues in contact with GLN 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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10A GLY* 5.7 1.3 - - - -
86A THR* 2.8 22.9 + - + +
87A GLU* 3.1 19.7 + - - +
89A TYR* 1.3 74.7 - - - +
91A GLN* 1.3 67.4 + - - +
93A ASN* 3.1 12.6 + - - +
94A ASP* 3.1 45.0 + - - +
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Residues in contact with GLN 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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8A SER 5.7 1.4 + - - -
10A GLY* 3.3 20.2 + - - +
11A SER* 2.9 29.9 - - - +
14A THR* 3.7 13.5 - - - +
60A ILE* 3.2 27.1 - - + +
87A GLU* 3.0 27.5 + - - +
90A GLN* 1.3 77.7 - - - +
92A LEU* 1.3 56.0 + - - +
94A ASP* 3.6 18.8 - - - +
95A LEU* 2.9 41.8 + - + +
151A PHE* 5.0 1.4 - - - -
155A THR* 5.4 1.0 - - - +
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Residues in contact with LEU 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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57A HIS* 3.1 63.0 + - + +
60A ILE* 3.5 23.8 - - + +
61A GLN* 4.0 11.4 - - + +
64A PHE* 4.3 15.0 - - + -
88A LEU 2.9 28.2 + - - +
89A TYR* 3.6 24.0 - - + +
90A GLN 3.1 0.2 - - - -
91A GLN* 1.3 76.4 - - - +
93A ASN* 1.3 59.2 + - - +
96A GLU* 2.9 31.6 + - - +
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Residues in contact with ASN 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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89A TYR* 2.8 21.8 + - + +
90A GLN* 3.1 13.2 + - - +
92A LEU* 1.3 74.4 - - - +
94A ASP* 1.3 69.6 + - - +
96A GLU* 3.3 11.3 + - - +
97A ALA* 2.9 29.4 + - - +
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Residues in contact with ASP 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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4A PRO* 4.4 24.3 - - + +
6A THR* 5.8 1.1 + - - -
7A HIS 5.2 5.9 - - - +
90A GLN* 3.1 34.7 + - - +
91A GLN* 3.6 18.7 - - - +
93A ASN* 1.3 79.4 + - - +
95A LEU* 1.3 68.0 + - + +
97A ALA* 3.1 20.8 + - - +
98A CYS* 3.6 11.4 + - - -
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Residues in contact with LEU 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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53A ILE* 3.1 52.4 - - + +
56A LEU* 3.4 50.3 - - + +
57A HIS* 3.5 20.4 - - + +
60A ILE* 3.7 17.0 - - + -
91A GLN* 2.9 31.4 + - + +
92A LEU* 4.5 1.1 - - - +
94A ASP* 1.3 77.4 - - + +
96A GLU* 1.3 61.9 + - - +
98A CYS 3.8 0.2 + - - -
99A VAL* 3.3 14.2 + - - +
158A GLN* 5.8 2.0 - - - +
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Residues in contact with GLU 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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57A HIS* 3.7 20.3 + - + +
92A LEU 2.9 19.7 + - - +
93A ASN* 3.7 12.0 - - - +
94A ASP 3.1 0.2 - - - -
95A LEU* 1.3 76.4 - - - +
97A ALA* 1.3 55.0 + - - +
99A VAL* 2.8 12.6 + - + -
100A ILE* 2.7 60.2 + - + +
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Residues in contact with ALA 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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3A LEU* 3.9 28.6 - - + +
4A PRO* 4.3 11.0 - - + -
93A ASN* 2.9 17.4 + - - +
94A ASP* 3.1 13.4 + - - +
96A GLU* 1.3 75.4 - - - +
98A CYS* 1.3 63.4 + - - +
100A ILE* 3.1 24.7 + - - +
101A GLN* 3.4 5.0 + - - +
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Residues in contact with CYS 98 (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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1A CYS* 2.0 46.9 - - + -
3A LEU* 3.7 12.6 - - - -
4A PRO* 4.5 10.8 - - - -
53A ILE* 3.4 26.9 - - + -
94A ASP 3.6 9.5 + - - -
96A GLU 3.2 0.6 - - - -
97A ALA* 1.3 78.3 - - - +
99A VAL* 1.3 57.9 + - - +
100A ILE 3.3 0.3 + - - -
101A GLN 3.1 2.4 - - - +
103A VAL* 2.7 35.6 - - + +
104A GLY* 4.6 5.2 - - - -
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Residues in contact with VAL 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 4.6 3.6 - - + -
54A PRO* 4.4 27.4 - - + -
57A HIS* 5.3 5.4 - - + -
95A LEU 3.3 17.7 - - - +
96A GLU* 2.8 21.3 + - + +
98A CYS* 1.3 71.2 - - + +
100A ILE* 1.3 66.4 + - + +
101A GLN 3.1 6.6 - - - +
103A VAL 4.1 4.7 - - - +
104A GLY* 5.1 4.3 - - - -
105A VAL* 5.1 17.7 - - + +
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Residues in contact with ILE 100 (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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96A GLU* 2.7 56.5 + - + +
97A ALA* 3.1 12.5 + - - +
99A VAL* 1.3 77.1 - - + +
101A GLN* 1.3 81.1 + - - +
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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
------------------------------------------------------------
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