Contacts of the strand formed by residues 121 - 128 (chain C) in PDB entry 2I6A
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 GLY 121 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C PRO 4.4 3.0 + - - -
16C LEU* 3.6 13.4 - - - -
17C LEU 3.1 17.8 + - - -
89C CYS 5.5 0.2 + - - -
119C PRO 3.2 2.2 + - - -
120C THR* 1.3 86.4 - - - +
122C THR* 1.3 60.2 + - - +
137C ASN* 3.3 5.8 - - - -
138C LEU 2.9 28.7 + - - -
139C ALA* 4.0 2.5 - - - -
140C ALA 4.1 1.0 - - - +
141C ALA 4.3 3.6 - - - +
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Residues in contact with THR 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU* 4.0 4.6 - - - +
17C LEU* 3.3 12.8 - - + +
19C ILE* 3.4 29.1 - - + +
49C PHE* 3.9 17.2 - - - -
95C PHE* 3.8 28.7 - - + -
120C THR 4.1 4.5 - - - +
121C GLY* 1.3 80.8 - - - +
123C CYS* 1.3 58.4 + - - +
136C ALA* 3.7 2.6 - - - +
137C ASN* 2.7 45.6 + - - +
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Residues in contact with CYS 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C LEU* 4.4 4.9 - - + -
17C LEU 3.0 6.2 + - - +
18C ASP* 3.5 20.5 - - - +
19C ILE* 2.9 28.2 + - - +
49C PHE* 4.4 1.8 - - - -
122C THR* 1.3 76.0 - - - +
124C ALA* 1.3 71.5 + - - +
125C ALA* 3.9 0.8 + - - +
134C LEU* 3.9 14.4 - - - -
135C ILE 3.5 6.7 - - - -
136C ALA* 3.8 16.2 - - + -
500C 5I5 3.8 36.8 - - - +
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Residues in contact with ALA 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C ILE* 3.2 6.3 - - + -
48C LEU* 3.9 20.9 - - + -
49C PHE* 3.8 20.2 - - + -
52C LEU* 3.9 17.5 - - + -
123C CYS* 1.3 73.7 - - - +
125C ALA* 1.3 60.9 + - - +
126C CYS* 3.7 3.8 - - - -
133C SER 3.4 0.4 - - - +
134C LEU* 3.1 11.3 - - - +
135C ILE* 2.9 37.9 + - + -
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Residues in contact with ALA 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ASP* 5.7 4.0 - - + -
19C ILE 2.8 9.7 + - - +
20C SER* 3.4 22.4 - - - -
21C ALA 3.3 12.8 + - - -
52C LEU* 5.0 1.9 - - - +
123C CYS* 5.2 1.6 - - - +
124C ALA* 1.3 73.3 - - - +
126C CYS* 1.3 60.0 + - - +
127C ILE* 3.0 21.2 + - + +
132C ARG* 3.9 15.7 - - - +
134C LEU* 3.6 23.3 - - + -
332C ARG* 5.6 2.7 - - - +
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Residues in contact with CYS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA 4.0 4.3 - - - -
23C VAL* 3.9 16.3 - - + +
27C PHE* 3.7 30.1 - - - -
28C LEU* 4.4 7.9 - - + +
33C LEU* 4.3 4.3 - - - -
35C PRO 4.2 1.9 - - - +
48C LEU* 4.9 1.8 - - - -
52C LEU* 4.4 11.0 - - - -
124C ALA* 4.4 7.2 - - - -
125C ALA* 1.3 70.5 - - - +
127C ILE* 1.3 62.6 + - - +
128C THR* 3.8 3.1 + - - +
132C ARG* 3.7 1.4 - - - -
133C SER* 3.0 42.1 + - - +
135C ILE* 3.9 20.6 - - - -
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Residues in contact with ILE 127 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C SER* 3.8 11.9 - - - -
21C ALA 3.1 27.8 + - - +
22C VAL* 3.3 20.6 - - + +
23C VAL* 2.7 29.2 + - - +
125C ALA 3.0 26.9 - - - +
126C CYS* 1.3 72.9 - - - +
128C THR* 1.3 66.0 + - - +
129C GLY 3.6 20.0 - - - +
131C ASN 3.4 10.8 - - - +
132C ARG* 3.6 32.8 - - + +
334C THR* 4.5 13.0 - - - +
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Residues in contact with THR 128 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C VAL* 5.0 1.8 - - - -
23C VAL* 3.5 29.8 - - + +
24C ASP 4.3 7.2 - - - +
25C LYS* 4.6 1.8 - - + +
28C LEU* 3.8 31.3 - - + +
35C PRO* 4.4 4.7 + - - +
126C CYS 3.8 2.5 + - - +
127C ILE* 1.3 79.7 - - - +
129C GLY* 1.3 55.2 + - - +
131C ASN* 2.7 51.5 + - - +
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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