Contacts of the strand formed by residues 121 - 127 (chain X) in PDB entry 1M6E
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 CYS 121 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74X ILE* 3.9 21.1 - - - -
92X TYR* 3.5 10.1 - - + +
94X ILE* 4.2 19.3 - - + -
116X ASP* 4.9 4.3 - - - +
117X VAL* 2.9 51.6 - - + +
118X ASP 3.6 18.8 - - - -
120X VAL* 1.3 77.8 - - - +
122X PHE* 1.3 63.3 + - - +
123X ILE* 3.1 9.6 + - + +
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Residues in contact with PHE 122 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91X GLU* 3.5 31.2 - - + -
92X TYR 3.0 16.2 + - - +
93X GLN* 3.8 13.4 - - + +
94X ILE 3.0 25.9 + - - +
116X ASP* 5.5 6.1 - - - -
120X VAL* 3.6 38.8 - - + -
121X CYS* 1.3 72.7 - - - +
123X ILE* 1.3 61.7 + - - +
124X ASN* 3.6 10.0 + - - +
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Residues in contact with ILE 123 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67X LEU* 3.7 35.9 - - + -
94X ILE* 3.8 23.6 - - + +
96X LEU* 3.9 25.6 - - + -
108X PHE* 4.7 11.9 - - + -
112X PRO* 3.9 22.0 - - + -
114X GLU* 5.5 1.8 - - - +
117X VAL* 4.9 10.8 - - + -
121X CYS* 3.1 11.3 + - + +
122X PHE* 1.3 74.7 - - - +
124X ASN* 1.3 74.2 + - - +
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Residues in contact with ASN 124 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93X GLN* 3.7 15.0 - - - +
94X ILE 2.8 21.3 + - - +
95X PHE* 3.2 36.3 - - + -
96X LEU* 2.7 32.9 + - - +
108X PHE* 5.5 0.2 - - - -
122X PHE* 3.6 14.1 + - - +
123X ILE* 1.3 86.3 - - - +
125X GLY* 1.3 56.9 + - - +
126X VAL* 5.1 0.4 - - + -
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Residues in contact with GLY 125 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96X LEU* 3.2 10.1 - - - -
104X PHE* 4.0 8.5 - - - -
108X PHE* 3.7 31.5 - - - -
124X ASN* 1.3 74.1 - - - +
126X VAL* 1.3 59.6 + - - +
127X PRO* 3.5 11.6 - - - +
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Residues in contact with VAL 126 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95X PHE* 3.5 36.8 - - + -
96X LEU 2.7 14.0 + - - +
97X ASN* 2.9 31.4 + - + +
98X ASP 3.6 0.8 + - - -
104X PHE* 4.2 1.5 - - - -
124X ASN* 4.4 1.3 - - + +
125X GLY* 1.3 75.7 - - - +
127X PRO* 1.3 62.2 - - + +
134X LEU* 4.1 38.4 - - + +
135X PHE* 3.6 12.6 - - + -
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Residues in contact with PRO 127 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97X ASN* 4.4 0.2 - - - -
98X ASP 3.3 8.5 - - - +
100X PRO* 4.3 23.1 - - + -
104X PHE* 4.4 15.5 - - + -
125X GLY 3.5 11.4 - - - +
126X VAL* 1.3 87.3 - - + +
128X GLY* 1.3 57.7 + - - +
134X LEU* 4.7 1.2 - - - +
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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