Contacts of the helix formed by residues 91 - 102 (chain G) in PDB entry 2EHO
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6G VAL* 3.9 4.0 - - + -
9G LEU* 3.9 34.5 - - + +
10G ALA* 3.4 34.1 - - + -
13G GLU* 3.9 31.4 - - + -
89G SER* 2.8 8.1 + - - +
90G PRO* 1.3 101.7 - - + +
92G TYR* 1.3 57.2 + - - +
94G GLU* 3.0 26.7 - - - +
95G LEU* 2.8 28.5 + - + +
149G THR* 5.6 0.7 - - - -
150G LEU* 3.9 27.8 - - + +
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Residues in contact with TYR 92 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G TRP* 4.2 12.1 - + + -
87G MSE 3.5 41.1 - - + -
88G PRO* 4.2 9.9 - - + -
89G SER* 2.9 32.5 + - - +
91G TYR* 1.3 75.7 - - - +
93G MSE 1.3 93.5 + - + +
95G LEU* 3.8 0.6 - - - +
96G THR* 2.9 29.4 + - - -
117G VAL* 3.7 32.1 - - + -
120G MSE 4.4 7.6 - - + -
121G TRP* 3.8 18.3 + + - +
124G ARG* 3.6 10.4 - - - -
149G THR* 4.4 9.2 - - + -
152G GLU* 3.0 29.8 + - + -
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Residues in contact with MSE 93 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92G TYR* 1.3 99.3 - - + +
94G GLU* 1.3 69.1 + - - +
96G THR* 3.4 6.5 + - + -
97G LYS* 2.9 32.6 + - + +
117G VAL* 4.6 7.4 - - + -
118G LYS* 5.0 14.1 - - + -
121G TRP* 3.7 55.4 - - + -
149G THR* 6.0 0.9 - - - +
151G MSE 4.9 5.4 - - + -
152G GLU* 6.3 0.2 - - + -
186H PHE* 4.8 7.2 - - + -
189H TRP* 3.7 27.8 - - + -
190H GLU* 5.7 4.3 - - + +
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Residues in contact with GLU 94 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G VAL* 3.6 13.7 - - - +
7G GLU* 4.3 17.0 - - - +
10G ALA* 3.7 21.5 - - + -
90G PRO 4.8 1.0 - - - +
91G TYR* 3.0 35.9 - - - +
93G MSE 1.3 78.7 + - - +
95G LEU* 1.3 64.4 + - - +
96G THR 3.2 0.4 - - - -
97G LYS* 4.2 0.2 - - - -
98G LEU* 3.0 31.7 + - + +
149G THR* 5.6 2.0 + - - -
150G LEU* 5.3 0.2 - - - +
151G MSE 3.1 33.0 + - + +
189H TRP* 3.7 27.8 - - + -
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Residues in contact with LEU 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G ALA* 4.6 4.0 - - + +
13G GLU* 4.5 24.2 - - + +
14G LEU 5.9 2.7 - - - +
15G VAL* 5.6 4.9 - - + -
46G LEU* 3.9 32.1 - - + -
63G PRO* 5.7 2.5 - - + -
65G TRP* 4.0 20.4 - - + +
89G SER* 2.9 32.5 - - - +
91G TYR* 2.8 20.5 + - + +
92G TYR 3.8 3.4 - - - +
94G GLU* 1.3 72.9 - - - +
96G THR* 1.3 53.5 + - - +
98G LEU* 4.2 2.1 - - - +
99G LEU* 2.8 52.7 + - + +
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Residues in contact with THR 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65G TRP* 3.1 29.3 - - - -
66G MSE 4.4 5.2 - - - +
92G TYR 2.9 13.0 + - - -
93G MSE 3.7 6.1 - - + +
95G LEU* 1.3 75.9 - - - +
97G LYS* 1.3 67.4 + - - +
98G LEU 3.1 0.4 + - - -
100G LEU* 3.2 52.3 + - + +
113G ILE* 4.6 4.3 - - + +
114G ARG* 4.9 2.9 - - - -
117G VAL* 3.9 32.1 - - + +
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Residues in contact with LYS 97 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G GLU* 3.3 34.5 + - - +
93G MSE 2.9 22.8 + - + +
94G GLU 3.9 2.7 - - - +
95G LEU 3.5 0.2 - - - -
96G THR* 1.3 76.8 - - - +
98G LEU* 1.3 65.4 + - + +
100G LEU* 4.0 1.3 - - - +
101G ASN* 2.8 49.3 + - - +
189H TRP* 3.6 51.7 + - + +
190H GLU* 4.6 9.6 - - + +
192H GLY* 4.4 11.3 - - - +
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Residues in contact with LEU 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G GLU* 3.5 33.7 - - + +
10G ALA* 5.9 1.8 - - + -
11G GLU* 4.3 15.0 - - + +
46G LEU* 3.7 31.4 - - + -
50G ILE* 4.2 9.9 - - + +
94G GLU* 3.0 21.3 + - + +
95G LEU* 4.2 1.3 - - - +
97G LYS* 1.3 90.5 - - + +
99G LEU* 1.3 57.9 + - - +
100G LEU 2.9 10.5 + - - -
101G ASN* 3.9 3.6 - - + +
102G HIS* 3.0 52.1 + - + +
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Residues in contact with LEU 99 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G VAL* 4.5 6.5 - - + -
46G LEU* 4.1 19.3 - - + -
50G ILE* 4.8 2.7 - - + -
60G LEU* 3.9 30.1 - - + -
62G PRO* 5.0 1.8 - - + -
63G PRO* 3.3 39.9 - - + -
66G MSE 4.0 6.3 - - - -
95G LEU* 2.8 37.9 + - + +
96G THR 3.6 0.4 + - - -
98G LEU* 1.3 72.5 - - - +
100G LEU* 1.3 61.1 + - + +
103G ALA* 3.1 30.8 - - + +
107G ILE* 2.9 27.8 - - + +
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Residues in contact with LEU 100 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66G MSE 3.3 31.4 - - + -
96G THR* 3.2 28.4 + - + +
97G LYS* 4.3 1.3 - - - +
98G LEU 2.9 0.4 - - - -
99G LEU* 1.3 87.5 - - + +
101G ASN* 1.3 62.4 + - - +
102G HIS 3.0 5.6 + - - -
104G SER* 3.6 27.3 - - - +
107G ILE* 3.4 9.2 - - + -
110G ALA* 4.3 9.6 - - - +
114G ARG* 3.3 61.9 + - + +
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Residues in contact with ASN 101 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97G LYS* 2.8 46.4 + - - +
98G LEU* 3.8 8.8 - - + +
100G LEU* 1.3 77.9 - - - +
102G HIS* 1.3 82.5 + - + +
104G SER* 5.5 0.4 - - - -
192H GLY* 5.1 6.1 - - - -
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Residues in contact with HIS 102 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50G ILE* 3.6 34.0 - - + +
53G LYS* 4.3 16.0 - - + +
54G GLN* 2.9 33.3 + - + +
98G LEU* 3.0 34.3 + - + +
101G ASN* 1.3 98.3 + - + +
103G ALA* 1.3 58.7 + - - +
104G SER* 3.1 14.7 + - - -
105G ASP* 4.5 2.8 - - - +
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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