Contacts of the strand formed by residues 121 - 128 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PRO 4.4 3.0 + - - -
16B LEU* 3.4 16.4 - - - -
17B LEU 3.1 19.6 + - - -
89B CYS 5.6 0.2 + - - -
119B PRO 3.4 0.6 + - - -
120B THR* 1.3 83.3 - - - +
122B THR* 1.3 62.5 + - - +
137B ASN 3.3 2.2 - - - -
138B LEU 2.7 30.7 + - - -
139B ALA* 3.8 1.8 - - - -
140B ALA* 4.0 4.0 - - - +
141B ALA 4.4 1.4 - - - +
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Residues in contact with THR 122 (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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16B LEU* 3.8 4.7 - - - +
17B LEU* 3.5 18.6 - - + +
19B ILE* 3.8 24.5 - - + -
49B PHE* 4.2 12.5 - - - -
95B PHE* 4.1 23.1 - - + -
120B THR 4.2 5.4 + - - +
121B GLY* 1.3 80.1 - - - +
123B CYS* 1.3 56.7 + - - +
124B ALA 4.3 0.4 - - - -
136B ALA* 3.4 2.3 - - - +
137B ASN* 2.5 56.3 + - - +
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Residues in contact with CYS 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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16B LEU* 4.2 8.5 - - + +
17B LEU 3.4 4.9 + - - -
18B ASP* 3.4 19.6 - - - +
19B ILE* 2.8 31.5 + - - -
49B PHE* 4.4 0.7 - - - -
122B THR* 1.3 75.3 - - - +
124B ALA* 1.3 57.3 + - - +
125B ALA* 3.8 1.0 + - - +
134B LEU* 3.8 24.7 - - - -
135B ILE 3.3 19.3 - - - -
136B ALA* 3.9 5.6 - - - -
500B 5I5 3.7 36.1 - - - +
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Residues in contact with ALA 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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19B ILE* 3.3 7.4 - - - +
48B LEU* 3.9 22.0 - - + -
49B PHE* 3.6 22.3 - - + -
52B LEU* 4.1 14.4 - - + -
123B CYS* 1.3 71.8 - - - +
125B ALA* 1.3 61.4 + - - +
126B CYS* 3.7 8.7 - - - -
133B SER 3.3 0.9 - - - +
134B LEU* 2.9 28.8 - - - +
135B ILE* 2.8 17.4 + - + +
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Residues in contact with ALA 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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18B ASP* 5.6 5.4 - - + -
19B ILE 2.9 10.8 + - - +
20B SER* 3.4 19.1 - - - -
21B ALA 3.4 20.3 + - - +
52B LEU* 5.8 0.4 - - - -
123B CYS 3.8 2.2 + - - +
124B ALA* 1.3 72.5 - - - +
126B CYS* 1.3 59.2 + - - +
127B ILE* 3.3 11.6 + - - +
132B ARG* 3.8 18.8 - - + +
133B SER 3.6 1.1 - - - -
134B LEU* 3.2 25.8 - - + -
332B ARG* 5.9 0.9 - - - +
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Residues in contact with CYS 126 (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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21B ALA 4.0 3.6 - - - +
23B VAL* 3.9 22.1 - - + +
27B PHE* 3.8 24.5 - - - -
28B LEU* 4.0 13.0 - - + +
33B LEU* 4.4 3.1 - - - -
35B PRO 4.6 1.0 - - - +
48B LEU* 4.4 3.4 - - - -
52B LEU* 4.6 6.3 - - - -
124B ALA* 4.1 15.0 - - - -
125B ALA* 1.3 65.9 - - - +
127B ILE* 1.3 61.5 + - - +
128B THR* 3.9 3.3 + - - +
131B ASN 3.9 0.2 - - - +
132B ARG* 3.9 1.4 - - - -
133B SER* 2.8 42.6 + - - +
135B ILE* 3.9 17.0 - - - -
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Residues in contact with ILE 127 (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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20B SER* 4.5 10.3 - - - -
21B ALA 2.9 20.7 + - - +
22B VAL* 3.2 20.7 - - + +
23B VAL* 2.8 28.0 + - - +
125B ALA 3.5 14.4 - - - +
126B CYS* 1.3 72.5 - - - +
128B THR* 1.3 67.3 + - - +
129B GLY 3.8 18.2 - - - +
130B ASP* 5.4 0.4 - - - -
131B ASN 3.4 11.7 - - - +
132B ARG* 3.2 38.4 - - + +
292B ILE* 6.2 5.2 - - + -
334B THR* 3.8 22.7 - - - +
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Residues in contact with THR 128 (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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22B VAL* 5.1 1.1 - - - -
23B VAL* 3.7 24.9 - - + +
24B ASP* 4.5 5.8 - - - +
25B LYS* 4.8 1.8 - - - +
28B LEU* 3.6 32.6 - - + +
35B PRO* 4.5 4.9 + - - +
126B CYS 3.9 1.5 + - - +
127B ILE* 1.3 79.3 - - - +
129B GLY* 1.3 57.7 + - - +
130B ASP 2.7 0.5 + - - -
131B ASN* 2.7 55.3 + - - +
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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