Contacts of the helix formed by residues 87 - 98 (chain A) in PDB entry 1TF6
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 LYS 87 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A PHE* 3.2 41.7 - - + -
76A ASP* 5.0 10.8 + - - +
86A THR* 1.3 71.9 - - - +
88A ALA* 1.3 61.4 + - - +
89A ASN 2.6 14.6 + - - -
90A MET* 2.7 30.0 + - + +
91A LYS* 2.7 13.8 + - + +
39C C 5.4 0.4 - - + -
40C C 2.9 38.3 + - - +
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Residues in contact with ALA 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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86A THR* 4.9 2.3 - - + +
87A LYS* 1.3 81.4 - - - +
89A ASN* 1.3 63.7 + - - +
91A LYS* 3.1 24.5 - - - +
92A LYS* 3.8 5.5 + - - +
40C C 4.0 31.0 - - + -
41C C 3.7 33.4 - - + +
42C A 6.0 1.1 - - - -
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Residues in contact with ASN 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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84A PHE* 4.6 4.8 - - - -
85A THR* 4.0 17.8 - - - +
86A THR* 3.1 36.1 + - - +
87A LYS 2.6 3.6 + - - -
88A ALA* 1.3 72.6 - - - +
90A MET* 1.3 58.9 + - - +
91A LYS 3.0 0.7 - - - -
92A LYS* 2.6 49.8 + - - +
93A HIS 4.1 0.2 + - - -
20B G 4.4 4.4 - - - +
21B G 3.4 24.3 + - - +
22B A 3.0 31.4 + - - +
23B T 5.6 2.5 - - - +
42C A 5.8 3.1 - - - +
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Residues in contact with MET 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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73A PHE* 5.4 2.0 - - + -
74A THR 2.8 25.8 - - - +
75A CYS* 3.4 13.0 - - + -
76A ASP* 3.6 28.9 - - + +
84A PHE* 3.2 47.1 - - + -
86A THR 2.9 16.0 + - - +
87A LYS* 2.7 23.8 + - + +
89A ASN* 1.3 76.4 - - - +
91A LYS* 1.3 73.2 + - + +
92A LYS 2.7 1.2 + - - -
93A HIS* 2.8 18.8 + - - +
94A PHE* 3.5 10.1 + - - -
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Residues in contact with LYS 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 LYS* 2.7 16.2 + - + +
88A ALA* 3.1 22.2 - - - +
90A MET* 1.3 82.7 - - + +
92A LYS* 1.3 64.6 + - + +
94A PHE* 3.7 4.4 + - - +
95A ASN* 3.4 43.3 + - - +
41C C 4.2 19.3 - - - +
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Residues in contact with LYS 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 ALA 4.6 4.0 - - - +
89A ASN* 2.6 42.4 + - - +
90A MET 2.7 0.2 + - - -
91A LYS* 1.3 71.3 - - + +
93A HIS* 1.3 67.8 + - - +
95A ASN* 3.0 9.7 + - - +
96A ARG* 2.9 59.3 + - - +
20B G 3.8 12.6 + - - -
21B G 2.7 31.5 + - - -
22B A 3.7 3.2 - - - +
42C A 5.6 0.7 - - - +
43C T 3.0 31.3 + - + +
44C C 4.4 1.8 - - - +
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Residues in contact with HIS 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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75A CYS* 3.0 17.9 - - + -
80A CYS* 3.4 6.9 - - + -
82A LEU* 6.5 0.2 - - + -
84A PHE* 3.3 37.9 - + + -
90A MET* 2.8 14.1 + - - +
92A LYS* 1.3 72.7 - - - +
94A PHE* 1.3 61.6 + - + +
96A ARG* 2.6 31.2 + - - +
97A PHE* 2.8 38.1 + + + +
98A HIS* 2.8 9.5 + + - -
114A LYS* 5.7 1.6 - - - -
203A ZN 2.0 37.8 - - - -
20B G 4.0 24.3 + - - +
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Residues in contact with PHE 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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75A CYS* 4.7 1.1 - - - -
76A ASP* 2.9 31.0 - - + -
77A SER* 3.4 24.9 - - - -
78A ASP 5.2 0.4 - - - -
90A MET* 3.5 11.5 + - - +
91A LYS* 3.8 10.1 - - - +
92A LYS 3.3 0.2 - - - -
93A HIS* 1.3 80.5 - - + +
95A ASN* 1.3 60.7 - - - +
97A PHE 2.6 22.9 + - - -
98A HIS* 2.7 36.9 + + + -
99A ASN* 3.2 44.2 + - + -
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Residues in contact with ASN 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 LYS* 3.4 41.2 + - - +
92A LYS* 3.0 9.3 + - - +
94A PHE* 1.3 87.4 - - - +
96A ARG* 1.3 59.0 + - + +
97A PHE 3.1 2.8 + - - -
99A ASN* 3.8 21.2 - - + +
102A ILE* 3.1 30.4 - - + +
103A CYS* 4.1 0.3 - - - -
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Residues in contact with ARG 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 LYS* 2.9 56.7 + - - +
93A HIS* 2.6 17.6 + - - +
95A ASN* 1.3 73.6 - - + +
97A PHE* 1.3 63.7 + - + +
103A CYS* 4.9 3.3 - - - +
19B T 3.7 53.5 + - - +
20B G 3.2 49.5 + - - +
43C T 6.0 1.4 - - - +
44C C 6.0 0.4 - - - +
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Residues in contact with PHE 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 HIS* 3.5 35.2 - + + +
94A PHE 2.6 10.6 + - - +
95A ASN 3.1 2.0 + - - -
96A ARG* 1.3 78.8 - - + +
98A HIS* 1.3 69.8 + + + +
103A CYS* 3.1 26.1 - - - +
114A LYS* 3.1 50.7 - - + -
115A ALA* 3.8 26.7 - - - +
19B T 6.0 1.3 - - - -
20B G 5.2 9.0 - - - -
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Residues in contact with HIS 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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77A SER* 3.1 16.0 + - - -
78A ASP 4.5 9.0 + - - -
80A CYS* 3.7 11.9 - - + -
93A HIS* 2.8 13.7 + + - -
94A PHE* 2.7 47.7 + + + -
97A PHE* 1.3 86.6 - + + +
99A ASN* 1.3 69.3 + - - +
100A ILE* 2.8 17.8 + - - +
103A CYS* 3.9 2.9 - - - +
106A VAL* 5.8 0.3 - - - +
113A GLY 5.3 4.5 + - - -
114A LYS* 4.8 8.6 - - - -
115A ALA* 5.1 3.8 - - - +
203A ZN 2.0 37.2 - - - -
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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