Contacts of the strand formed by residues 91 - 98 (chain M) in PDB entry 5X6E
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 GLN 91 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21M GLN* 3.9 28.5 - - + +
22M PHE 3.4 8.7 - - - +
23M HIS* 3.9 22.3 + - - +
43M ASP* 4.5 6.4 - - - +
44M GLY* 4.4 3.8 - - - -
89M SER* 3.1 10.0 + - - -
90M GLU* 1.3 89.5 - - + +
92M ALA* 1.3 60.7 + - - +
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Residues in contact with ALA 92 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21M GLN* 3.0 5.5 - - - +
22M PHE* 2.9 35.6 + - + +
28M ILE* 6.0 0.9 - - + -
41M LEU* 4.4 10.8 - - + -
43M ASP* 3.2 13.0 - - - +
44M GLY* 3.6 8.5 - - - -
45M ILE 4.3 0.9 - - - +
46M THR* 4.7 3.4 - - + -
87M VAL* 3.8 18.6 - - + +
89M SER* 3.4 18.2 - - - +
91M GLN* 1.3 71.4 - - - +
93M THR* 1.3 60.5 - - - +
94M ALA 3.9 0.7 + - - -
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Residues in contact with THR 93 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M PRO* 3.9 20.3 - - - +
20M LYS 3.8 3.3 + - - -
21M GLN* 2.9 26.3 + - - +
41M LEU* 3.6 3.1 - - - +
42M TYR* 3.1 42.3 + - + +
43M ASP* 2.7 46.9 + - + +
92M ALA* 1.3 72.5 - - - +
94M ALA* 1.3 63.7 + - - +
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Residues in contact with ALA 94 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19M PRO* 4.6 0.4 - - - -
20M LYS* 2.9 34.9 + - - +
22M PHE* 3.9 23.4 - - + -
28M ILE* 4.3 9.2 - - + -
39M ILE* 4.4 12.1 - - + -
40M PHE 3.5 10.8 - - - +
41M LEU* 4.3 13.7 - - + -
42M TYR 4.4 0.2 - - - +
92M ALA* 3.9 0.6 + - + +
93M THR* 1.3 77.0 + - - +
95M TYR* 1.3 66.6 + - - +
96M VAL* 3.8 2.5 + - + -
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Residues in contact with TYR 95 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9M LYS* 3.4 34.9 + - + +
12M LEU* 3.5 31.6 - - + -
13M GLU* 3.7 19.9 + - + +
17M ILE* 3.2 33.0 - - + -
18M LYS 4.0 1.8 - - - -
19M PRO* 3.4 38.4 - - + +
38M CYS 3.8 0.5 - - - +
39M ILE* 3.6 6.1 - - - +
40M PHE* 2.9 52.4 + + + +
42M TYR* 4.3 16.3 - + + -
93M THR* 4.6 1.8 - - - -
94M ALA* 1.3 75.3 - - - +
96M VAL* 1.3 61.5 + - - +
97M ILE* 3.7 3.9 + - + +
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Residues in contact with VAL 96 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17M ILE* 4.4 9.2 - - - +
18M LYS 5.3 2.6 + - - -
20M LYS* 5.0 7.7 - - + +
22M PHE* 3.8 33.7 - - + -
28M ILE* 4.2 12.6 - - + +
37M TYR* 3.6 38.8 - - + -
38M CYS 4.2 1.6 - - - -
39M ILE* 4.9 6.7 - - + -
94M ALA* 3.8 4.2 + - + +
95M TYR* 1.3 74.6 - - - +
97M ILE* 1.3 63.6 + - - +
98M LYS* 5.6 1.8 - - + +
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Residues in contact with ILE 97 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8M PHE* 5.7 5.8 - - + -
12M LEU* 4.8 13.0 - - + -
17M ILE* 3.7 36.1 - - + -
37M TYR* 3.4 12.3 - - - +
38M CYS* 3.2 64.5 + - + +
40M PHE* 6.1 2.0 - - + +
95M TYR 4.6 6.3 - - - +
96M VAL* 1.3 78.5 - - - +
98M LYS* 1.3 67.7 + - - +
101M GLU* 5.1 6.3 - - + +
102M LEU* 3.7 27.1 - - + -
105M LEU* 4.8 8.3 - - + -
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Residues in contact with LYS 98 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35M GLN* 5.9 5.3 - - - +
36M GLU 4.5 4.9 - - - -
37M TYR* 4.8 18.7 - - + -
96M VAL* 5.6 1.8 - - + +
97M ILE* 1.3 80.8 - - - +
99M ILE* 1.3 64.7 + - - +
100M ASN* 3.5 12.1 + - + +
101M GLU* 3.1 39.1 + - + +
102M LEU* 3.8 13.9 + - - +
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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