Contacts of the strand formed by residues 121 - 128 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15A PRO 4.3 4.2 + - - -
16A LEU* 3.5 14.3 - - - -
17A LEU 3.0 19.6 + - - -
89A CYS 5.6 0.4 + - - -
119A PRO 3.5 0.8 + - - -
120A THR* 1.3 83.9 - - - +
122A THR* 1.3 64.2 + - - +
137A ASN 3.3 3.6 - - - -
138A LEU 3.1 27.4 + - - -
139A ALA* 4.2 0.9 - - - -
140A ALA* 4.3 2.8 - - - +
141A ALA 4.6 1.2 - - - +
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Residues in contact with THR 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.1 4.9 - - - +
17A LEU* 3.4 16.2 - - + +
19A ILE* 3.8 24.1 - - + +
49A PHE* 3.8 14.1 - - - -
95A PHE* 3.8 25.6 - - + -
120A THR 4.5 3.8 - - - +
121A GLY* 1.3 81.0 - - - +
123A CYS* 1.3 57.6 + - - +
136A ALA* 3.5 3.3 - - - +
137A ASN* 2.7 52.8 + - - +
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Residues in contact with CYS 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LEU* 4.0 7.2 - - + -
17A LEU 3.2 5.3 + - - -
18A ASP* 3.3 21.1 - - - +
19A ILE* 2.7 34.1 + - - +
49A PHE* 4.5 2.2 - - - -
122A THR* 1.3 75.9 - - - +
124A ALA* 1.3 60.4 + - - +
125A ALA* 3.9 0.4 + - - -
134A LEU* 3.9 24.2 - - - -
135A ILE 3.6 13.7 - - - -
136A ALA* 3.9 4.5 - - - -
500A 5I5 3.7 36.8 - - - +
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ILE* 3.3 6.5 - - - -
48A LEU* 4.0 12.8 - - + -
49A PHE* 3.5 23.2 - - + -
52A LEU* 3.8 21.8 - - + -
123A CYS* 1.3 74.1 - - - +
125A ALA* 1.3 60.0 + - - +
126A CYS* 3.7 7.9 - - - -
133A SER 3.3 1.6 - - - +
134A LEU* 3.1 9.7 - - - +
135A ILE* 2.9 33.9 + - + +
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Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASP* 5.6 5.4 - - + -
19A ILE 2.9 10.5 + - - +
20A SER* 3.5 18.3 - - - -
21A ALA 3.3 20.6 + - - +
52A LEU* 5.5 0.4 - - - +
123A CYS 3.9 1.7 + - - +
124A ALA* 1.3 71.3 - - - +
126A CYS* 1.3 61.1 + - - +
127A ILE* 3.2 10.6 + - - +
132A ARG* 3.8 20.0 - - + +
133A SER 3.7 0.9 - - - +
134A LEU* 3.3 25.1 - - + -
332A ARG* 5.7 0.7 - - - +
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Residues in contact with CYS 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ALA 3.8 4.9 - - - -
23A VAL* 3.7 21.1 - - + +
27A PHE* 4.0 22.2 - - + -
28A LEU* 4.3 12.6 - - + +
33A LEU* 4.7 1.3 - - - -
35A PRO 4.7 1.0 - - - +
48A LEU* 4.6 2.0 - - - -
52A LEU* 4.5 9.2 - - - -
124A ALA* 4.1 13.2 - - - -
125A ALA* 1.3 70.6 - - - +
127A ILE* 1.3 62.5 + - - +
128A THR* 4.0 3.1 + - - +
132A ARG* 4.0 0.7 + - - -
133A SER* 3.0 32.0 + - - +
135A ILE* 3.7 26.9 - - - -
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Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A SER* 4.9 4.7 - - - -
21A ALA 2.9 17.3 + - - +
22A VAL* 3.4 15.8 - - + +
23A VAL* 2.7 30.5 + - - +
125A ALA 3.6 13.7 - - - +
126A CYS* 1.3 69.2 - - - +
128A THR* 1.3 68.9 + - - +
129A GLY 3.7 17.0 - - - +
130A ASP 5.1 0.9 - - - -
131A ASN 2.9 23.3 - - - +
132A ARG* 2.8 39.3 - - + +
292A ILE* 6.2 5.4 - - + -
334A THR* 3.7 23.1 - - - +
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Residues in contact with THR 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A VAL* 4.8 2.2 - - - -
23A VAL* 3.4 33.0 - - + +
24A ASP 4.6 3.8 - - - +
25A LYS* 5.0 1.3 - - - +
28A LEU* 4.1 22.1 - - + +
35A PRO* 4.4 9.6 + - - +
126A CYS 4.0 2.2 + - - +
127A ILE* 1.3 84.8 - - - +
129A GLY* 1.3 63.3 + - - +
130A ASP 3.1 0.5 + - - -
131A ASN* 3.0 36.1 + - - +
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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