Contacts of the helix formed by residues 80 - 98 (chain A) in PDB entry 5TE0
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 ASN 80 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78A VAL* 3.4 3.1 - - - +
79A ASN* 1.3 98.0 + - - +
81A GLU* 1.3 59.3 + - - +
82A HIS* 3.4 12.5 + - - +
83A ASP* 2.8 49.5 + - - +
84A LEU* 3.0 27.7 + - - +
120A TRP* 3.7 12.2 - - - -
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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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80A ASN* 1.3 71.5 - - - +
82A HIS* 1.3 57.5 + - - +
84A LEU* 3.6 15.4 - - - +
85A GLN* 2.8 36.6 + - - +
120A TRP* 3.5 24.9 - - + -
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Residues in contact with HIS 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASN* 3.4 9.3 + - - +
81A GLU* 1.3 78.1 - - - +
83A ASP* 1.3 71.8 + - - +
85A GLN* 3.4 7.0 + - - +
86A VAL* 3.0 39.8 + - + +
216A GLU* 3.4 33.8 + - - -
219A LYS* 4.6 8.3 - - + +
220A TYR* 3.2 22.8 + - - -
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Residues in contact with ASP 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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78A VAL* 3.6 24.3 - - + -
79A ASN* 4.5 2.6 + - - +
80A ASN* 2.8 32.1 + - - +
82A HIS* 1.3 88.8 - - - +
84A LEU* 1.4 64.2 + - - +
86A VAL* 3.3 9.1 + - - +
87A CYS* 3.1 26.7 + - - -
219A LYS* 4.0 18.5 + - - -
220A TYR* 4.2 2.1 + - - -
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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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78A VAL* 3.3 9.1 - - + +
80A ASN 3.0 18.7 + - - +
81A GLU* 3.2 19.3 + - - +
83A ASP* 1.4 71.7 - - - +
85A GLN* 1.3 61.4 + - - +
87A CYS* 3.2 6.2 + - + +
88A LYS* 2.9 51.4 + - + +
111A ILE* 3.8 20.2 - - + -
120A TRP* 3.7 58.1 - - + +
122A VAL* 4.7 7.2 - - + -
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Residues in contact with GLN 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 2.8 21.6 + - - +
82A HIS* 3.6 8.5 - - - +
84A LEU* 1.3 69.2 - - - +
86A VAL* 1.3 57.6 + - + +
88A LYS* 3.2 15.1 + - - +
89A ARG* 2.8 68.4 + - - +
201A LYS* 5.7 1.2 - - - +
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Residues in contact with VAL 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 HIS* 3.0 30.1 + - + +
83A ASP* 3.3 10.9 + - - +
85A GLN* 1.3 77.1 - - + +
87A CYS* 1.4 58.5 + - - +
89A ARG* 3.5 8.8 + - + +
90A GLU* 3.0 26.3 + - - +
195A PHE 5.1 0.5 - - - +
196A GLY* 3.3 29.8 - - - +
198A ALA 5.9 2.5 - - - +
220A TYR* 3.3 32.8 - - + +
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Residues in contact with CYS 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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76A MET* 4.2 19.7 - - - -
78A VAL* 3.6 23.1 - - - -
83A ASP 3.1 18.3 + - - +
84A LEU* 3.2 8.7 + - + +
86A VAL* 1.4 76.3 - - - +
88A LYS* 1.3 59.7 + - + +
90A GLU* 3.2 11.5 + - - +
91A ILE* 3.0 34.9 + - + +
111A ILE* 5.4 1.3 - - + -
122A VAL* 4.0 31.2 - - + -
124A ILE* 5.9 2.0 - - + -
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Residues in contact with LYS 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 LEU* 2.9 42.1 + - + +
85A GLN* 3.2 16.4 + - - +
87A CYS* 1.3 73.8 - - - +
89A ARG* 1.4 56.7 + - - +
91A ILE* 3.5 6.8 + - - +
92A GLN* 3.0 30.0 + - - +
111A ILE* 3.6 31.6 - - + -
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Residues in contact with ARG 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 GLN* 2.8 40.3 + - - +
86A VAL* 3.5 9.2 - - + +
88A LYS* 1.4 73.2 - - - +
90A GLU* 1.4 66.2 + - - +
92A GLN* 3.3 17.0 + - - +
93A ILE* 3.0 52.5 + - + +
172A ILE* 5.0 2.4 - - - +
195A PHE 5.3 1.1 - - - +
198A ALA* 3.7 22.4 - - + +
199A THR* 4.6 6.5 + - - +
200A ASN* 3.2 42.9 + - - +
201A LYS* 3.9 10.9 - - - +
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Residues in contact with GLU 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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74A LYS* 3.5 22.7 + - - +
76A MET* 5.6 2.6 - - - +
86A VAL 3.0 15.1 + - - +
87A CYS* 3.2 12.8 + - - +
89A ARG* 1.4 77.9 - - - +
91A ILE* 1.3 61.9 + - - +
93A ILE* 3.3 3.1 + - - +
94A MET* 3.0 34.8 + - - +
124A ILE* 4.1 18.6 - - + +
194A ASP* 3.9 4.2 - - - +
195A PHE* 3.1 41.5 + - + +
196A GLY* 3.6 17.0 + - - +
401A XIN 4.1 15.1 - - - +
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Residues in contact with ILE 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 CYS 3.0 19.3 + - - +
88A LYS* 3.9 4.5 - - - +
89A ARG 3.4 0.2 - - - -
90A GLU* 1.3 74.5 - - - +
92A GLN* 1.3 59.0 + - - +
94A MET* 3.2 8.6 + - - +
95A ARG* 2.8 55.5 + - + +
106A TYR* 4.1 4.7 - - + +
109A SER* 3.3 35.2 - - - +
111A ILE* 4.0 27.8 - - + -
122A VAL* 4.1 18.2 - - + -
123A LEU 4.9 0.4 - - - +
124A ILE* 3.7 20.4 - - + -
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Residues in contact with GLN 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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88A LYS 3.0 18.2 + - - +
89A ARG* 3.7 18.8 - - - +
90A GLU 3.3 0.2 - - - -
91A ILE* 1.3 74.3 - - - +
93A ILE* 1.4 64.9 + - - +
95A ARG* 3.2 20.3 + - - +
96A ASP* 2.9 64.0 + - - +
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Residues in contact with ILE 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 ARG* 3.0 45.6 + - + +
90A GLU* 3.7 3.8 - - - +
92A GLN* 1.4 73.8 - - + +
94A MET* 1.3 56.0 - - - +
96A ASP* 3.2 4.6 + - - -
97A LEU* 2.8 55.5 + - + +
165A LEU* 5.1 0.2 - - + -
172A ILE* 3.9 28.9 - - + -
195A PHE* 3.9 33.7 - - + -
198A ALA* 3.5 28.5 - - + -
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Residues in contact with MET 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 GLU* 3.0 33.0 + - - +
91A ILE* 3.5 4.9 - - - +
93A ILE* 1.3 74.9 - - - +
95A ARG* 1.3 64.5 + - - +
98A SER* 2.9 42.4 + - - +
104A VAL 4.3 6.5 - - - +
105A GLY 4.4 0.2 - - - +
106A TYR* 3.8 33.9 - - + +
124A ILE* 4.1 15.5 - - + -
126A MET* 3.7 20.6 - - + -
195A PHE* 3.8 18.4 - - + -
401A XIN 3.6 32.3 - - - +
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Residues in contact with ARG 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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91A ILE* 2.8 41.7 + - - +
92A GLN* 3.6 22.7 - - - +
94A MET* 1.3 73.3 - - - +
96A ASP* 1.3 67.6 + - - +
98A SER 4.9 0.3 + - - -
106A TYR* 2.8 53.4 + - + -
108A ASP* 5.1 4.2 + - - -
109A SER* 3.8 8.3 + - - +
111A ILE* 6.2 1.0 - - - +
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Residues in contact with ASP 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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92A GLN* 2.9 46.4 + - - +
93A ILE* 3.8 3.5 - - - +
95A ARG* 1.3 82.9 - - - +
97A LEU* 1.3 74.2 + - + +
99A GLY 5.4 0.6 + - - -
164A ARG* 4.3 8.1 + - - -
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Residues in contact with LEU 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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93A ILE* 2.8 34.5 + - + +
96A ASP* 1.3 89.2 - - + +
98A SER* 1.3 59.3 + - - +
99A GLY 3.2 2.9 - - - -
100A HIS* 3.0 29.2 + - - +
103A ILE* 3.6 11.1 - - + +
164A ARG* 3.6 37.6 + - + +
165A LEU* 4.0 24.5 - - + -
168A CYS* 4.1 31.2 - - + -
172A ILE* 4.3 10.3 - - + -
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Residues in contact with SER 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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93A ILE 4.1 0.2 + - - -
94A MET* 2.9 43.6 + - - +
96A ASP 3.9 0.2 - - - -
97A LEU* 1.3 70.6 - - - +
99A GLY* 1.3 60.9 + - - +
100A HIS 3.0 3.8 - - - +
103A ILE* 3.0 24.0 - - - +
104A VAL 3.2 20.3 + - - -
105A GLY* 3.8 2.6 - - - -
106A TYR* 3.5 19.4 - - - +
409A GOL 2.9 22.0 + - - -
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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