Contacts of the helix formed by residues 92 - 104 (chain H) in PDB entry 3ECS
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 ILE 92 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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78H LEU* 3.8 32.3 - - + -
89H CYS* 2.9 33.9 - - - +
90H LYS* 2.5 23.7 + - + +
91H LYS* 1.3 73.0 - - - +
93H MSE 1.3 64.8 + - - +
94H ILE 3.2 1.3 - - - -
95H GLU* 2.7 43.3 - - + +
96H ARG* 3.2 15.0 + - - +
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Residues in contact with MSE 93 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34H LEU* 4.0 13.6 - - + +
43H GLN 5.7 4.0 - - - +
46H ARG* 3.0 33.4 - - - +
47H ALA* 5.8 7.2 - - + -
73H LEU* 5.0 6.1 - - + -
76H ILE* 2.9 58.6 - - + +
77H SER* 3.7 18.8 - - - +
78H LEU* 4.4 14.1 - - + -
90H LYS* 2.9 29.5 + - - +
91H LYS* 4.7 2.2 - - - -
92H ILE* 1.3 82.4 - - - +
94H ILE* 1.3 51.6 - - - +
96H ARG* 3.1 5.9 + - - +
97H GLY* 2.6 34.0 + - - -
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Residues in contact with ILE 94 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H LEU* 3.8 17.9 - - + +
34H LEU* 3.5 35.2 - - + +
35H LYS* 3.6 38.4 - - + +
91H LYS* 3.9 28.0 - - + +
92H ILE 3.2 0.2 - - - -
93H MSE 1.3 77.7 - - - +
95H GLU* 1.3 57.2 + - - +
97H GLY* 3.1 2.7 + - - -
98H GLU* 2.8 45.5 + - - +
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Residues in contact with GLU 95 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91H LYS 4.6 1.3 + - - +
92H ILE* 2.7 40.0 - - + +
94H ILE* 1.3 76.7 - - + +
96H ARG* 1.3 82.5 + - - +
98H GLU* 3.4 17.0 + - - +
99H LEU* 3.1 22.3 + - - +
102H ARG* 4.5 3.1 + - - -
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Residues in contact with ARG 96 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H PHE* 3.1 39.9 + - + -
76H ILE* 4.1 10.1 - - - +
77H SER 3.4 17.8 + - - -
78H LEU* 3.1 39.5 - - - +
92H ILE* 3.4 13.2 - - - +
93H MSE 3.1 10.4 + - - +
95H GLU* 1.3 97.0 + - - +
97H GLY* 1.3 59.1 + - - +
99H LEU* 3.0 10.6 + - + +
100H PHE 2.9 25.5 + - - -
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Residues in contact with GLY 97 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H LEU* 4.0 4.5 - - - -
72H PHE* 3.4 30.7 - - - -
76H ILE* 3.5 4.7 - - - +
93H MSE 2.6 19.0 + - - -
94H ILE* 3.1 6.2 + - - -
96H ARG* 1.3 75.3 - - - +
98H GLU* 1.3 59.6 + - - +
100H PHE* 3.6 3.3 - - - +
101H LEU* 3.4 27.0 + - - +
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Residues in contact with GLU 98 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31H LEU* 3.6 20.4 - - + -
35H LYS* 3.6 25.3 + - - -
94H ILE* 2.8 26.8 + - - +
95H GLU* 3.7 17.9 - - - +
96H ARG 3.1 0.4 - - - -
97H GLY* 1.3 74.1 - - - +
99H LEU* 1.3 64.1 + - - +
101H LEU* 3.8 4.1 + - - +
102H ARG* 2.9 41.1 + - - +
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Residues in contact with LEU 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H PHE* 3.9 21.1 - - + -
95H GLU* 3.1 14.9 + - - +
96H ARG* 3.0 14.5 + - + +
98H GLU* 1.3 75.2 - - - +
100H PHE* 1.3 55.4 + - - +
102H ARG* 3.2 27.7 + - + +
103H ARG* 2.8 79.3 + - + +
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Residues in contact with PHE 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27H ILE* 5.0 4.3 - - + -
68H GLY 4.5 3.1 - - - -
71H LEU* 3.9 30.3 - - + -
72H PHE* 3.5 44.4 - + + -
75H PHE* 3.7 34.8 - + + -
96H ARG 2.9 11.5 + - - +
97H GLY* 3.6 11.0 - - - +
99H LEU* 1.3 74.7 - - - +
101H LEU* 1.3 62.0 + - + +
103H ARG* 2.9 12.4 + - + +
104H ILE* 2.8 61.8 + - + +
233H PHE* 5.1 5.2 - - + -
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Residues in contact with LEU 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H VAL* 4.3 2.7 - - + +
27H ILE* 3.3 42.6 - - + +
28H ARG* 3.1 49.4 - - + +
31H LEU* 3.3 35.7 - - + -
72H PHE* 5.3 2.2 - - + -
97H GLY 3.4 9.0 + - - +
98H GLU* 4.0 5.2 - - - +
99H LEU 3.4 0.2 - - - -
100H PHE* 1.3 79.6 - - + +
102H ARG* 1.3 57.9 + - - +
103H ARG 3.2 0.5 + - - -
104H ILE* 3.4 11.8 + - + +
105H SER* 2.5 30.2 + - - -
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Residues in contact with ARG 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95H GLU 4.5 3.8 + - - -
98H GLU* 2.9 42.5 + - - +
99H LEU* 3.2 41.0 - - + +
101H LEU* 1.3 79.8 - - - +
103H ARG* 1.3 62.1 + - + +
105H SER* 3.3 6.4 - - - -
106H LEU* 3.1 23.8 - - + +
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Residues in contact with ARG 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75H PHE* 5.3 8.3 - - + -
99H LEU* 2.8 63.0 + - + +
100H PHE* 2.9 15.4 + - + +
102H ARG* 1.3 74.9 - - + +
104H ILE* 1.3 56.5 + - + +
105H SER 2.5 18.9 + - - -
106H LEU* 3.3 16.6 + - - +
107H SER* 4.4 1.9 + - - -
110H LYS* 5.8 1.0 + - - -
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Residues in contact with ILE 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24H VAL* 4.5 16.2 - - + +
27H ILE* 3.1 35.7 - - + -
100H PHE* 2.8 55.1 + - + +
101H LEU* 3.6 10.5 - - + +
103H ARG* 1.3 69.1 - - + +
105H SER* 1.3 57.2 + - - +
106H LEU 3.7 0.9 - - - -
107H SER* 3.7 19.6 + - - +
232H SER* 5.4 5.8 - - - +
233H PHE* 4.1 36.7 - - + -
287H ASP* 5.8 0.7 - - - +
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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