Contacts of the helix formed by residues 91 - 104 (chain F) in PDB entry 2E9X
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 TYR 91 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F VAL* 3.9 14.6 - - + -
9F LEU* 3.7 17.9 - - + +
10F ALA* 3.4 42.0 - - + -
13F GLU* 3.6 34.3 - - + -
89F SER* 3.0 7.1 + - - +
90F PRO* 1.3 96.8 - - + +
92F TYR* 1.3 62.9 + - - +
94F GLU* 3.1 29.8 - - - +
95F LEU* 3.0 30.8 + - + +
149F THR* 5.3 0.7 - - - -
150F LEU* 4.2 19.7 - - + +
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Residues in contact with TYR 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F TRP* 3.7 24.1 - + + -
71F LEU* 6.4 0.9 - - + -
87F MET* 3.6 42.6 - - + -
88F PRO* 4.6 5.6 - - + -
89F SER* 3.4 21.2 + - - +
91F TYR* 1.3 76.7 - - - +
93F MET* 1.3 84.8 + - + +
96F THR* 2.6 34.3 + - - -
117F VAL* 3.7 24.5 - - + -
120F MET* 4.4 9.4 - - + -
121F TRP* 3.7 14.6 - - - +
124F ARG* 3.6 9.9 + - - -
149F THR* 3.9 9.6 - - + -
152F GLU* 2.8 34.6 + - - -
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Residues in contact with MET 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F TYR 3.3 0.4 - - - -
92F TYR* 1.3 110.6 - - + +
94F GLU* 1.3 65.5 + - - +
96F THR* 3.4 2.6 + - - -
97F LYS* 2.9 31.3 + - + +
117F VAL* 3.7 17.0 - - + +
118F LYS* 5.6 2.5 - - - -
121F TRP* 3.5 40.6 - - + -
149F THR* 5.5 0.2 - - - +
151F MET* 4.6 11.4 - - + -
152F GLU* 5.3 0.4 - - + -
186G PHE* 3.9 28.3 - - + -
189G TRP* 4.0 10.2 - - + -
190G GLU* 4.3 11.0 - - + +
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Residues in contact with GLU 94 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F VAL* 3.1 27.4 - - - +
7F GLU* 3.9 11.7 - - + -
10F ALA* 3.4 26.7 - - + -
90F PRO 5.0 0.3 - - - +
91F TYR* 3.1 35.0 - - - +
93F MET* 1.3 76.0 + - - +
95F LEU* 1.3 59.9 + - - +
97F LYS* 3.3 0.3 + - - +
98F LEU* 2.9 37.9 + - + +
149F THR* 5.8 0.3 + - - -
151F MET* 3.2 35.5 + - + +
189G TRP* 3.7 16.8 - - + -
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Residues in contact with LEU 95 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ALA* 4.1 10.5 - - + +
13F GLU* 4.3 14.1 - - + +
14F LEU 5.6 1.6 - - - +
15F VAL* 4.9 10.1 - - + -
46F LEU* 3.6 30.5 - - + -
63F PRO* 4.6 11.0 - - + -
65F TRP* 4.0 23.8 - - + +
66F MET* 4.1 4.9 - - + -
89F SER* 3.8 19.1 - - - +
91F TYR* 3.0 32.7 + - + +
92F TYR 4.2 0.2 - - - +
94F GLU* 1.3 76.6 - - - +
96F THR* 1.3 58.7 + - - +
99F LEU* 2.9 40.0 + - + +
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Residues in contact with THR 96 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65F TRP* 3.6 11.4 - - - -
66F MET* 3.8 9.6 - - + +
92F TYR 2.6 24.4 + - - -
93F MET 3.7 3.8 - - - -
95F LEU* 1.3 76.1 - - - +
97F LYS* 1.3 64.1 + - - +
100F LEU* 2.9 54.2 + - + +
113F ILE* 4.3 7.9 - - + +
114F ARG* 4.7 2.7 - - + -
117F VAL* 3.5 40.5 - - + +
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Residues in contact with LYS 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F GLU* 2.7 36.0 + - - +
93F MET* 2.9 19.1 + - + +
94F GLU 3.7 2.9 - - - +
96F THR* 1.3 77.8 - - - +
98F LEU* 1.3 72.8 + - + +
100F LEU* 5.1 0.4 - - - -
101F ASN* 3.0 52.1 + - - +
114F ARG* 5.4 4.9 - - - +
189G TRP* 3.5 47.6 + - + +
190G GLU* 4.4 12.8 - - + +
192G GLY* 4.2 12.0 - - - +
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Residues in contact with LEU 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F GLU* 3.4 44.4 - - + +
11F GLU* 4.0 18.2 - - + +
46F LEU* 3.9 27.6 - - + -
50F ILE* 3.9 18.7 - - + +
94F GLU* 2.9 19.8 + - + +
95F LEU 4.3 1.1 - - - +
97F LYS* 1.3 82.1 - - + +
99F LEU* 1.3 67.1 + - - +
101F ASN* 3.3 2.1 + - + -
102F HIS* 3.1 47.8 + - + +
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Residues in contact with LEU 99 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15F VAL* 5.0 7.4 - - + -
46F LEU* 3.4 33.0 - - + -
50F ILE* 4.4 7.9 - - + -
60F LEU* 4.6 14.4 - - + -
61F LEU 4.7 4.9 - - - +
63F PRO* 3.4 37.2 - - + -
66F MET* 3.6 22.2 - - + -
95F LEU* 2.9 25.3 + - + +
96F THR 4.3 0.4 - - - +
98F LEU* 1.3 75.0 - - + +
100F LEU* 1.3 59.1 + - - +
103F ALA* 2.8 37.4 + - - +
107F ILE* 4.5 13.9 - - + -
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Residues in contact with LEU 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F MET* 4.9 2.5 - - - -
96F THR* 2.9 41.2 + - + +
97F LYS 4.4 0.2 - - - +
99F LEU* 1.3 77.7 - - + +
101F ASN* 1.3 60.6 + - - +
102F HIS 3.6 0.2 + - - -
104F SER* 3.3 24.1 + - - +
107F ILE* 4.0 22.0 - - + -
110F ALA* 3.7 33.2 - - + +
113F ILE* 4.5 5.4 - - + -
114F ARG* 3.4 65.2 + - + +
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Residues in contact with ASN 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F LYS* 3.0 45.3 + - + +
98F LEU* 3.8 4.0 - - + +
99F LEU 3.3 0.2 - - - -
100F LEU* 1.3 78.5 - - - +
102F HIS* 1.3 76.3 + - + +
104F SER* 5.2 0.4 - - - -
114F ARG* 3.7 22.7 + - - +
190G GLU 5.1 2.0 + - - -
191G LYS 4.5 14.3 + - - -
192G GLY* 4.6 4.4 + - - -
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Residues in contact with HIS 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50F ILE* 3.7 35.1 - - + +
53F LYS* 3.3 26.1 - - + +
54F GLN* 3.1 40.5 + - + +
98F LEU* 3.1 35.6 + - + +
101F ASN* 1.3 92.3 + - + +
103F ALA* 1.3 60.0 + - - +
104F SER 3.9 0.4 - - - -
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Residues in contact with ALA 103 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53F LYS* 3.9 8.1 - - - +
60F LEU* 3.4 39.0 - - + -
99F LEU* 2.8 20.2 + - - +
102F HIS* 1.3 76.5 - - - +
104F SER* 1.3 59.6 + - - +
105F ASP* 3.0 11.2 - - - -
106F ASN* 2.8 21.0 + - + +
107F ILE* 3.1 15.0 + - + +
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Residues in contact with SER 104 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99F LEU 3.6 2.5 + - - -
100F LEU* 3.3 21.0 + - - +
101F ASN 5.7 0.2 - - - -
102F HIS 3.9 0.6 - - - -
103F ALA* 1.3 76.8 - - - +
105F ASP* 1.3 60.0 + - - +
106F ASN 3.0 0.4 - - - -
107F ILE* 2.8 28.9 - - - +
110F ALA* 3.8 25.8 - - - +
114F ARG* 5.5 1.8 - - - -
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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