Contacts of the helix formed by residues 93 - 104 (chain B) in PDB entry 5E1M
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 THR 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B LYS* 4.9 3.0 + - - +
20B TRP* 3.6 19.5 - - - +
21B LYS* 4.4 12.8 + - + +
91B ASP* 2.9 14.7 + - - +
92B ILE* 1.3 81.4 - - - +
94B GLU* 1.3 66.1 + - - +
95B ASP* 4.0 11.4 - - + +
96B PHE* 3.0 44.7 + - + +
97B LEU* 3.5 9.6 + - - +
116B CYS* 4.3 1.6 - - - -
301B SAH 2.8 16.7 + - - -
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Residues in contact with GLU 94 (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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92B ILE 3.6 5.1 + - - -
93B THR* 1.3 71.5 - - - +
95B ASP* 1.3 68.7 + - - +
97B LEU* 3.0 13.9 + - - +
98B VAL* 3.0 37.2 + - + +
101B LYS* 5.7 1.6 + - - -
116B CYS* 3.3 33.1 - - - +
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Residues in contact with ASP 95 (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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77A LYS* 5.2 3.8 - - - -
78A ARG* 4.3 22.8 + - - +
21B LYS* 4.9 8.8 - - - +
25B PRO* 4.6 5.0 - - + +
93B THR* 3.3 10.5 - - + +
94B GLU* 1.3 81.9 - - - +
96B PHE* 1.3 63.0 + - + +
98B VAL* 3.7 11.6 - - - +
99B GLN* 2.9 28.6 + - - +
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Residues in contact with PHE 96 (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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20B TRP* 3.3 37.5 - + - -
21B LYS 5.8 0.4 - - - -
23B ILE* 3.4 23.3 - - + -
25B PRO* 3.9 20.0 - - + -
30B MET* 3.6 27.1 - - + -
71B GLY* 3.6 18.4 - - - -
72B ILE* 3.5 14.7 - - - +
91B ASP* 3.9 2.7 - - - +
93B THR* 3.0 29.5 + - + +
95B ASP* 1.3 79.7 - - + +
97B LEU* 1.3 59.0 + - - +
99B GLN* 3.3 2.0 + - - +
100B ALA 2.9 23.0 + - - -
301B SAH 3.2 35.0 - - - -
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Residues in contact with LEU 97 (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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70B ALA* 5.1 0.2 - - + -
71B GLY 3.9 15.5 - - - +
89B MET* 4.2 26.5 - - + -
91B ASP* 3.9 21.3 - - + +
93B THR 3.5 7.6 + - - +
94B GLU* 3.0 13.5 + - - +
96B PHE* 1.3 74.7 - - - +
98B VAL* 1.3 63.9 + - - +
100B ALA* 3.3 16.8 + - - +
101B LYS* 3.1 21.3 + - - +
114B TYR* 4.0 16.7 - - + -
115B PHE 3.3 37.2 - - - +
116B CYS* 3.7 18.4 - - + +
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Residues in contact with VAL 98 (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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94B GLU* 3.0 35.9 + - + +
95B ASP* 3.7 13.9 - - - +
97B LEU* 1.3 76.2 - - - +
99B GLN* 1.3 65.7 + - - +
101B LYS* 3.2 30.1 + - + +
102B THR* 4.0 4.2 + - - -
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Residues in contact with GLN 99 (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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25B PRO* 3.7 42.3 - - + +
72B ILE* 4.0 6.7 - - + -
95B ASP 2.9 19.2 + - - +
96B PHE 3.3 5.1 + - - +
98B VAL* 1.3 80.3 - - - +
100B ALA* 1.3 62.0 + - - +
102B THR* 2.9 22.3 + - - +
103B TYR* 2.9 19.3 + - + +
313B UNX 4.3 9.3 - - - -
319B UNX 2.7 28.0 - - - -
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Residues in contact with ALA 100 (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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72B ILE* 3.2 31.1 + - - +
89B MET* 3.8 19.5 - - + -
96B PHE 2.9 13.0 + - - +
97B LEU* 3.4 12.1 - - - +
98B VAL 3.2 0.6 - - - -
99B GLN* 1.3 75.3 - - - +
101B LYS* 1.3 57.4 + - - +
103B TYR* 4.1 1.6 - - - -
104B LEU* 2.8 39.7 + - + +
114B TYR* 4.0 8.7 - - + -
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Residues in contact with LYS 101 (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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94B GLU* 5.7 1.0 + - - -
97B LEU* 3.1 24.9 + - - +
98B VAL* 3.2 18.7 + - + +
99B GLN 3.1 1.0 + - - -
100B ALA* 1.3 77.0 - - - +
102B THR* 1.3 61.6 + - - +
104B LEU* 4.6 1.1 - - - +
105B GLY* 3.8 14.9 + - - +
108B GLY* 5.8 0.9 - - - -
114B TYR* 3.6 51.7 - - + +
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Residues in contact with THR 102 (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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98B VAL 4.0 3.0 + - - -
99B GLN* 2.9 28.7 + - - +
101B LYS* 1.3 77.8 - - - +
103B TYR* 1.3 67.1 + - - +
105B GLY* 3.1 14.9 + - - -
319B UNX 4.1 3.4 - - - -
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Residues in contact with TYR 103 (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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27B VAL* 3.4 30.7 - - + +
72B ILE* 3.3 38.8 - - + +
73B GLY 3.5 23.3 - - - -
74B ARG* 3.9 10.7 + - - +
77B LYS* 3.1 50.3 + - + +
78B ARG* 5.3 5.9 - - - -
99B GLN 2.9 17.3 + - - +
100B ALA* 4.0 0.7 - - - +
102B THR* 1.3 75.2 - - - +
104B LEU* 1.3 63.2 + - + +
105B GLY* 3.5 0.5 + - - -
319B UNX 3.4 21.5 - - - -
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Residues in contact with LEU 104 (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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72B ILE 4.3 3.1 - - - +
73B GLY 3.5 26.5 - - - +
76B THR* 4.0 5.2 - - + -
77B LYS* 3.6 37.7 + - + +
81B LEU* 4.3 3.4 - - + +
89B MET* 3.9 19.5 - - - -
100B ALA* 2.8 25.1 + - + +
101B LYS* 4.8 1.1 - - - +
103B TYR* 1.3 81.4 - - + +
105B GLY* 1.3 63.2 + - - +
106B GLU 3.6 0.2 + - - -
107B GLU* 3.6 8.3 + - - +
108B GLY* 3.2 22.1 + - - +
111B VAL* 3.8 28.3 - - + -
114B TYR* 4.2 5.8 - - - +
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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