Contacts of the helix formed by residues 72 - 88 (chain B) in PDB entry 1FTA
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 72 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56B LEU* 5.3 12.5 - - - +
73B LEU* 1.3 61.4 + - - +
74B ASP* 3.3 10.7 + - - -
75B VAL* 2.9 25.4 + - + +
76B LEU* 2.8 41.4 + - + +
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE 5.1 0.2 - - - +
47B ALA* 3.7 41.5 - - + +
48B VAL* 4.1 13.5 - - + +
50B LYS* 3.6 27.8 - - - +
72B LYS* 1.3 73.1 - - - +
74B ASP* 1.3 59.5 + - - +
76B LEU* 3.2 13.8 + - + +
77B SER* 2.8 38.8 + - - +
120B LEU* 4.0 12.1 - - + -
126B ILE* 3.9 26.5 - - + -
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Residues in contact with ASP 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS 4.2 12.1 + - - -
73B LEU* 1.3 74.3 + - - +
75B VAL* 1.3 64.5 + - - +
77B SER* 3.6 4.3 + - - -
78B ASN* 3.0 25.8 + - - +
98B GLU* 3.4 30.2 - - - +
119B PRO* 4.4 3.7 - - + +
120B LEU* 3.9 15.5 - - + +
123B SER* 3.9 31.5 + - - +
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Residues in contact with VAL 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS* 2.9 27.9 + - + +
74B ASP* 1.3 85.4 - - - +
76B LEU* 1.3 60.1 + - - +
78B ASN* 3.1 8.4 + - + +
79B ASP* 2.8 46.3 + - - +
98B GLU* 4.8 9.2 - - - +
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Residues in contact with LEU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47B ALA* 4.1 25.1 - - + -
72B LYS* 2.8 26.5 + - + +
73B LEU* 3.4 16.4 - - + +
75B VAL* 1.3 75.8 - - - +
77B SER* 1.3 58.3 + - - +
79B ASP* 2.9 11.0 + - + +
80B LEU* 2.8 48.9 + - + +
55C HIS* 5.0 14.6 - - + +
60C ALA* 4.5 13.2 - - + -
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Residues in contact with SER 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ILE* 3.6 28.2 - - - +
73B LEU* 2.8 22.1 + - - +
74B ASP 3.7 5.8 - - - -
76B LEU* 1.3 76.4 - - - +
78B ASN* 1.3 62.6 + - - -
80B LEU* 3.3 2.9 + - - +
81B VAL* 3.0 28.2 + - - +
119B PRO* 3.8 15.3 - - - -
120B LEU* 3.5 26.4 - - - +
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Residues in contact with ASN 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ASP 3.0 15.8 + - - +
75B VAL* 3.1 10.0 + - + +
77B SER* 1.3 75.6 - - - +
79B ASP* 1.3 70.4 + - - +
81B VAL* 3.2 1.3 + - - +
82B MET* 2.9 34.9 + - - +
96B SER* 2.7 27.8 + - - -
98B GLU* 3.8 19.5 - - + +
99B ASP* 3.4 21.4 + - - -
117B PHE* 3.7 5.0 - - - -
119B PRO* 3.3 21.5 - - + +
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Residues in contact with ASP 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B VAL* 2.8 37.1 + - - +
76B LEU* 2.9 11.4 + - + +
78B ASN* 1.3 80.8 + - - +
80B LEU* 1.3 58.1 + - - +
82B MET* 4.4 4.8 - - - +
83B ASN* 2.8 42.9 + - - +
60C ALA* 4.0 21.1 - - + +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ALA* 4.5 7.0 - - + +
43B ALA* 3.8 24.0 - - + +
44B ILE* 3.7 39.9 - - + +
47B ALA* 5.3 0.9 - - + -
76B LEU* 2.8 41.9 + - + +
77B SER* 3.7 4.5 - - - +
79B ASP* 1.3 69.8 - - - +
81B VAL* 1.3 62.6 + - - +
83B ASN 4.0 0.3 - - - -
84B MET* 3.0 30.7 + - + +
55C HIS* 4.5 8.3 - - - +
59C ILE* 3.9 21.9 - - + +
60C ALA* 3.8 25.4 - - + +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B LEU* 4.5 13.5 - - + -
40B ALA* 4.2 12.3 - - + -
44B ILE* 3.8 21.3 - - + -
77B SER 3.0 18.0 + - - +
78B ASN 3.8 2.9 - - - +
80B LEU* 1.3 74.5 - - - +
82B MET* 1.3 63.4 + - - +
84B MET* 3.1 2.1 + - - +
85B LEU* 2.9 51.1 + - + +
117B PHE* 3.8 29.8 - - + -
119B PRO* 4.5 7.9 - - + -
134B THR* 4.7 7.9 - - + -
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Residues in contact with MET 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ASN* 2.9 36.1 + - - +
79B ASP* 3.7 6.5 - - - +
81B VAL* 1.3 76.6 - - - +
83B ASN* 1.3 62.5 + - - +
85B LEU* 3.8 3.7 - - - +
86B LYS* 2.9 46.5 + - - +
94B LEU* 4.0 18.1 - - + +
99B ASP* 4.4 5.6 - - - +
103B ILE* 3.6 49.4 - - + -
117B PHE* 3.7 21.8 - - + -
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Residues in contact with ASN 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79B ASP* 2.8 34.6 + - - +
82B MET* 1.3 78.6 - - - +
84B MET* 1.3 63.2 + - - +
86B LYS* 3.8 10.8 - - - +
87B SER* 2.7 31.5 + - - +
58C GLY 5.6 0.2 - - - +
59C ILE 3.8 16.4 - - - +
60C ALA 2.9 21.6 + - - -
61C GLY* 3.5 20.8 - - - +
9D ASP 5.8 1.1 - - - +
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Residues in contact with MET 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36B SER* 3.7 23.6 - - - +
39B THR* 4.0 30.5 - - - -
40B ALA* 4.2 12.1 - - + -
80B LEU* 3.0 21.8 + - + +
81B VAL 3.1 2.9 + - - +
83B ASN* 1.3 75.8 - - - +
85B LEU* 1.3 62.5 + - + +
87B SER* 3.2 13.2 + - - +
88B SER 3.1 16.5 + - - -
58C GLY 5.5 0.2 - - - +
59C ILE* 3.9 22.9 - - + +
10D VAL* 3.5 25.8 - - + -
12D THR* 5.6 2.5 - - + -
15D ARG* 3.3 37.4 + - - +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 3.5 31.4 - - + +
36B SER* 4.9 0.9 - - - -
37B LEU* 3.6 25.8 - - + +
81B VAL* 2.9 39.5 + - + +
82B MET* 3.8 3.4 - - - +
84B MET* 1.3 74.6 - - + +
86B LYS* 1.3 66.7 + - - +
88B SER* 2.7 25.3 + - - -
91B THR* 3.5 11.2 + - + -
94B LEU* 3.6 30.7 - - + -
115B VAL* 3.9 19.5 - - + -
117B PHE* 4.0 6.3 - - + -
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Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B MET* 2.9 37.3 + - + +
83B ASN* 3.8 11.2 - - - +
85B LEU* 1.3 77.3 - - - +
87B SER* 1.3 63.4 + - - +
88B SER 3.0 0.7 + - - -
89B PHE* 3.1 13.9 + - - -
91B THR* 4.2 5.6 + - - -
94B LEU* 4.0 13.2 - - + -
103B ILE* 3.9 29.7 - - - +
105B VAL* 4.4 12.8 - - + -
106B GLU* 3.4 31.0 + - - +
109B LYS* 4.0 27.1 - - + +
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Residues in contact with SER 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B ASN* 2.7 18.3 + - - +
84B MET* 3.3 18.3 - - - +
86B LYS* 1.3 78.0 - - - +
88B SER* 1.3 55.4 + - - +
89B PHE* 3.0 26.1 - - - -
109B LYS* 5.1 7.5 - - - +
9D ASP* 4.9 13.0 + - - -
10D VAL 4.7 3.3 + - - -
15D ARG* 3.3 34.2 + - - -
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Residues in contact with SER 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B GLU* 5.8 0.3 - - - +
32B GLN* 3.8 23.4 - - - +
33B LEU* 3.7 8.6 - - - +
36B SER* 3.3 32.8 - - - -
84B MET 3.1 4.4 + - - -
85B LEU* 2.7 19.6 + - - -
86B LYS 3.0 0.8 + - - -
87B SER* 1.3 75.4 - - - +
89B PHE* 1.3 66.0 + - - +
90B ALA* 3.0 26.2 + - - +
91B THR 4.2 0.5 + - - -
15D ARG* 4.2 5.7 - - - +
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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