Contacts of the strand formed by residues 121 - 125 (chain B) in PDB entry 6CMO
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ALA* 4.6 9.9 - - - -
114B CYS 3.3 18.8 - - - +
115B GLY* 4.5 1.3 - - - -
119B ASN 4.2 0.8 + - - -
120B ILE* 1.3 71.9 - - - +
122B SER* 1.3 64.5 + - - +
123B ILE* 4.3 1.0 + - - -
137B ARG 4.1 0.2 - - - +
138B GLU* 3.7 1.6 - - - -
139B LEU* 2.9 53.6 + - + +
146B LEU* 4.1 16.7 - - + +
149B CYS* 4.2 23.3 - - - -
157B ILE* 5.4 4.5 - - - -
159B THR* 5.0 9.6 - - + -
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Residues in contact with SER 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B VAL 4.1 0.7 - - - +
113B ALA* 3.3 5.2 - - - +
114B CYS* 3.2 36.7 + - - -
120B ILE* 3.9 9.6 + - - +
121B CYS* 1.3 74.4 + - - +
123B ILE* 1.3 59.4 + - - +
124B TYR* 3.7 30.2 + - - -
135B VAL* 4.8 2.8 - - - +
137B ARG 3.6 9.0 - - - -
138B GLU* 3.9 17.5 + - - +
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Residues in contact with ILE 123 (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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111B TYR* 3.6 39.3 - - + -
112B VAL 3.7 7.6 - - - +
113B ALA* 4.2 8.5 - - + -
121B CYS* 4.3 1.1 - - - -
122B SER* 1.3 71.2 - - - +
124B TYR* 1.3 66.1 + - - +
136B SER* 2.8 46.0 + - - +
137B ARG* 3.7 21.6 + - + +
139B LEU* 5.3 10.5 - - + -
151B PHE* 3.9 19.7 - - + -
157B ILE* 5.4 1.1 - - + -
171B ILE* 4.2 30.5 - - + -
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Residues in contact with TYR 124 (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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79B LEU* 5.5 4.5 - - + -
93B ILE* 3.6 37.0 - - + -
94B PRO 4.6 1.5 + - - -
95B LEU* 3.7 25.2 - - + +
96B ARG 5.3 0.3 + - - -
111B TYR* 3.4 12.0 - - - -
112B VAL* 2.8 50.2 + - + +
114B CYS* 4.4 18.7 - - - -
122B SER* 3.7 27.7 + - - -
123B ILE* 1.3 82.0 - - - +
125B ASN* 1.3 60.5 + - - +
126B LEU 3.9 0.3 + - - -
133B VAL* 3.9 16.2 - - + -
134B ARG 3.7 13.7 - - - -
135B VAL* 3.6 28.5 - - + +
136B SER* 5.2 0.4 - - - -
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Residues in contact with ASN 125 (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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116A GLU* 5.6 3.4 + - - -
110B ASN* 5.4 0.9 - - - +
111B TYR* 3.8 23.6 - - + +
123B ILE 4.3 0.6 + - - -
124B TYR* 1.3 73.6 - - - +
126B LEU* 1.3 61.0 + - - +
127B LYS 4.9 2.9 - - - +
128B THR* 4.2 25.2 + - - +
133B VAL* 4.2 10.0 - - - +
134B ARG* 3.0 43.4 + - - +
136B SER* 4.8 14.8 - - - +
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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