Contacts of the helix formed by residues 81 - 102 (chain A) in PDB entry 1SFX
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 81 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A TYR* 3.8 0.2 - - - -
29A LEU* 4.4 19.0 + - + +
79A ALA 4.5 8.0 + - - +
80A GLU* 1.3 76.2 - - - +
82A PRO* 1.3 76.5 - - + +
83A GLU* 3.2 26.5 - - - +
84A LYS 3.0 11.6 + - - -
85A VAL* 3.0 10.2 + - - +
402A EDO 2.9 28.7 + - - +
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Residues in contact with PRO 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A TYR* 3.7 3.1 - - - +
29A LEU* 4.1 19.1 - - + -
81A LYS* 1.3 91.3 - - + +
83A GLU* 1.3 61.7 + - - +
85A VAL* 3.3 2.2 + - + +
86A LEU* 2.9 36.9 + - - +
4B PRO* 3.7 31.2 - - + -
104B PHE* 3.7 44.6 - - + -
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Residues in contact with GLU 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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81A LYS* 3.3 28.6 - - + +
82A PRO* 1.3 81.4 - - - +
84A LYS* 1.3 59.7 + - + +
86A LEU* 3.6 7.2 + - - +
87A LYS* 3.0 28.5 + - - +
402A EDO 5.1 5.7 - - - +
101B GLU* 4.9 5.4 - - - +
104B PHE* 5.5 3.7 - - - +
105B THR* 5.9 7.2 - - + -
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Residues in contact with LYS 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A GLY* 3.1 25.6 + - - +
80A GLU* 3.7 30.6 + - + +
81A LYS 3.0 6.1 + - - +
83A GLU* 1.3 80.9 - - + +
85A VAL* 1.3 65.6 + - - +
87A LYS* 3.3 25.0 + - - +
88A GLU* 3.0 47.3 + - - +
402A EDO 3.4 37.9 - - - +
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Residues in contact with VAL 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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25A TYR* 3.5 38.6 - - + +
62A PHE* 3.5 34.9 - - + +
80A GLU* 3.8 4.7 - - + +
81A LYS 3.0 10.9 + - - +
82A PRO* 3.3 9.2 + - + +
84A LYS* 1.3 76.1 - - - +
86A LEU* 1.3 59.6 + - - +
88A GLU* 3.4 0.4 + - - -
89A PHE* 2.9 27.7 + - - +
4B PRO* 4.3 11.7 - - + -
5B LEU* 3.5 29.8 - - + -
8B LEU* 4.5 5.4 - - + -
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Residues in contact with LEU 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 PRO 2.9 25.1 + - - +
83A GLU* 4.1 3.1 - - - +
85A VAL* 1.3 72.6 - - - +
87A LYS* 1.3 61.1 + - - +
89A PHE* 3.9 2.7 - - - +
90A LYS* 2.9 31.0 + - - +
4B PRO* 4.2 12.1 - - + -
8B LEU* 3.9 33.9 - - + -
97B ILE* 4.1 13.9 - - + +
100B ILE* 3.8 28.7 - - + +
101B GLU* 3.6 48.2 - - + +
104B PHE* 4.3 6.1 - - + -
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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 GLU 3.0 18.5 + - - +
84A LYS* 3.6 31.3 - - - +
86A LEU* 1.3 76.7 - - - +
88A GLU* 1.3 64.0 + - - +
90A LYS* 3.5 7.4 + - - +
91A SER* 3.0 28.5 + - - -
101B GLU* 4.3 5.7 + - - +
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Residues in contact with GLU 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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60A ARG 3.9 19.8 - - - +
61A GLY* 4.0 9.6 - - - +
62A PHE* 4.0 4.9 - - + -
84A LYS* 3.0 54.4 + - + +
85A VAL 3.7 3.6 - - - +
87A LYS* 1.3 82.2 - - - +
89A PHE* 1.3 65.6 + - - +
91A SER* 3.3 9.3 + - - -
92A SER* 3.0 29.4 + - - +
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Residues in contact with PHE 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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15A LEU* 3.8 35.4 - - + -
17A PHE* 4.0 18.6 - + - -
60A ARG* 3.9 16.2 - - - -
62A PHE* 4.2 7.7 - + + -
85A VAL 2.9 17.6 + - - +
86A LEU* 3.9 3.6 - - - +
88A GLU* 1.3 75.8 - - - +
90A LYS* 1.3 65.0 + - - +
92A SER* 3.1 7.2 + - - -
93A ILE* 2.9 34.8 + - + +
8B LEU* 3.9 29.6 - - + -
12B LEU* 3.8 33.2 - - + -
93B ILE* 4.6 3.4 - - + -
97B ILE* 3.8 21.8 - - + -
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Residues in contact with LYS 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 LEU 2.9 15.8 + - - +
87A LYS* 3.6 7.9 - - - +
89A PHE* 1.3 77.8 - - - +
91A SER* 1.3 62.9 + - - +
93A ILE* 3.4 1.6 + - - +
94A LEU* 3.0 38.7 + - + +
94B LEU* 3.6 28.7 - - + -
97B ILE* 3.7 36.3 - - + -
98B GLU* 4.2 15.0 + - - +
101B GLU* 3.2 28.4 + - - -
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Residues in contact with SER 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* 3.0 17.8 + - - -
88A GLU* 3.7 11.2 - - - -
90A LYS* 1.3 75.8 - - - +
92A SER* 1.3 59.3 + - - +
94A LEU* 3.6 6.5 + - - +
95A GLY* 3.0 25.3 + - - -
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Residues in contact with SER 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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15A LEU* 3.9 23.1 - - - +
60A ARG* 5.6 4.1 + - - -
88A GLU* 3.0 19.4 + - - +
89A PHE* 3.1 8.9 + - - -
91A SER* 1.3 77.6 - - - +
93A ILE* 1.3 60.7 + - - +
95A GLY* 3.3 2.5 + - - -
96A GLU* 3.1 25.8 + - - +
99A ARG* 4.7 2.5 + - - +
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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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8A LEU* 5.8 0.4 - - + -
11A ALA* 4.6 10.8 - - + +
12A LEU* 4.7 10.1 - - + -
15A LEU* 3.6 23.3 - - + +
89A PHE* 2.9 23.2 + - + +
90A LYS* 3.4 15.9 - - + +
92A SER* 1.3 73.4 - - - +
94A LEU* 1.3 73.1 + - + +
96A GLU* 3.2 8.8 + - + +
97A ILE* 3.0 41.3 + - + +
89B PHE* 4.7 6.3 - - + -
93B ILE* 3.9 28.9 - - + -
94B LEU* 5.6 0.4 - - + -
97B ILE* 4.1 16.2 - - + -
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Residues in contact with LEU 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 LYS* 3.0 31.1 + - + +
91A SER* 3.9 5.4 - - - +
93A ILE* 1.3 79.5 - - + +
95A GLY* 1.3 57.6 + - - +
97A ILE* 3.8 7.7 - - + +
98A GLU* 2.9 46.7 + - - +
90B LYS* 3.7 38.8 - - + +
93B ILE* 5.7 0.7 - - + -
94B LEU* 3.9 30.5 - - + -
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Residues in contact with GLY 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 SER 3.0 16.2 + - - -
92A SER* 3.7 4.3 - - - -
93A ILE 3.2 0.4 - - - -
94A LEU* 1.3 75.8 - - - +
96A GLU* 1.3 61.4 + - - +
98A GLU* 3.4 12.8 + - - +
99A ARG* 3.1 45.0 + - - +
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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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11A ALA* 3.6 32.8 - - + +
14A LYS* 3.1 37.1 + - - +
15A LEU* 4.2 20.0 - - + -
92A SER 3.1 16.5 + - - +
93A ILE* 3.2 11.6 + - + +
95A GLY* 1.3 76.4 - - - +
97A ILE* 1.3 61.7 + - - +
99A ARG* 3.2 28.5 + - - +
100A ILE* 3.0 31.5 + - - +
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Residues in contact with ILE 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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8A LEU* 4.3 15.9 - - + -
93A ILE* 3.0 38.7 + - + +
94A LEU* 3.8 7.2 - - + +
96A GLU* 1.3 75.7 - - - +
98A GLU* 1.3 58.8 + - - +
100A ILE* 3.1 8.7 + - + +
101A GLU* 2.8 37.5 + - + +
86B LEU* 4.6 19.5 - - + +
89B PHE* 3.9 22.4 - - + -
90B LYS* 3.6 45.3 - - + -
93B ILE* 4.3 3.8 - - + -
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Residues in contact with GLU 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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94A LEU* 2.9 34.8 + - - +
95A GLY* 3.6 11.5 - - - +
97A ILE* 1.3 78.1 - - - +
99A ARG* 1.3 62.9 + - + +
101A GLU* 3.5 31.3 - - - +
102A LYS* 3.7 18.8 - - - +
90B LYS* 4.7 10.1 + - - +
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Residues in contact with ARG 99 (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 LYS* 4.6 6.6 - - - +
92A SER* 4.7 2.0 + - - +
95A GLY* 3.1 31.3 + - - +
96A GLU* 3.2 36.8 + - - +
97A ILE 3.2 0.2 - - - -
98A GLU* 1.3 76.5 - - + +
100A ILE* 1.3 65.7 + - + +
102A LYS* 3.1 32.8 + - + +
103A MSE 4.0 5.2 + - - +
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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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4A PRO 5.0 0.2 - - - +
7A GLU* 3.6 55.4 - - + +
8A LEU* 4.1 13.9 - - + +
11A ALA* 4.0 16.4 - - + -
96A GLU* 3.0 19.1 + - - +
97A ILE* 3.1 7.4 + - + +
99A ARG* 1.3 78.5 - - + +
101A GLU* 1.3 65.0 + - - +
103A MSE 2.9 26.0 + - - +
104A PHE* 3.3 18.8 - - + -
86B LEU* 3.9 19.1 - - + -
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Residues in contact with GLU 101 (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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97A ILE* 2.8 22.8 + - + +
98A GLU* 3.5 23.9 - - - +
99A ARG 3.2 0.6 - - - -
100A ILE* 1.3 77.6 - - - +
102A LYS* 1.3 58.5 + - + +
104A PHE* 3.0 18.0 + - - +
105A THR* 3.4 16.0 + - + +
83B GLU* 5.1 2.4 - - + +
86B LEU* 3.9 26.5 - - + +
87B LYS* 6.2 0.2 - - - -
90B LYS* 2.7 35.9 + - - -
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Residues in contact with LYS 102 (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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98A GLU* 3.7 18.8 - - - +
99A ARG* 3.1 20.9 + - + +
100A ILE 3.1 1.0 + - - -
101A GLU* 1.3 77.7 - - + +
103A MSE 1.3 60.2 + - + +
104A PHE 3.2 0.6 + - - -
105A THR* 4.0 20.0 + - + +
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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
------------------------------------------------------------
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