Contacts of the strand formed by residues 88 - 93 (chain A) in PDB entry 2LDX
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 SER 88 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A LYS* 3.5 16.6 - - - +
23A THR* 2.4 32.3 + - - -
85A SER 3.1 8.8 + - - -
87A ASN* 1.3 80.6 - - - +
89A LYS* 1.3 64.6 + - - +
90A LEU 4.1 5.8 - - - -
91A VAL* 3.9 18.8 - - - -
127A SER* 3.3 25.1 + - - -
129A ASP 5.1 1.2 - - - +
130A CYS* 4.0 8.0 + - - -
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Residues in contact with LYS 89 (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 ARG* 2.5 53.0 + - - +
20A CYS* 3.2 32.5 - - + +
21A LYS 2.9 14.1 + - - +
22A ILE* 5.6 0.2 - - + -
87A ASN* 2.9 23.2 + - - +
88A SER* 1.3 75.5 + - - +
90A LEU* 1.3 60.1 + - - +
129A ASP 4.9 1.4 - - - +
130A CYS* 3.9 2.3 - - - +
131A LYS* 3.1 29.9 + - - +
263A LEU* 4.7 15.7 - - + -
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Residues in contact with LEU 90 (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 LYS 3.4 2.2 + - - -
22A ILE* 3.5 26.7 - - + -
23A THR 3.0 25.6 + - - +
38A ILE* 4.9 2.5 - - + -
88A SER* 4.3 1.4 - - - -
89A LYS* 1.3 78.7 - - - +
91A VAL* 1.3 65.8 + - - +
92A ILE* 4.1 15.5 - - + -
131A LYS* 3.3 24.2 - - + +
133A ILE* 3.3 44.0 - - + -
259A ALA* 4.1 16.4 - - + -
262A ILE* 3.7 18.8 - - + -
263A LEU* 4.4 10.8 - - + -
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Residues in contact with VAL 91 (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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23A THR* 3.7 18.6 - - + -
25A VAL* 4.4 17.3 - - + -
85A SER* 4.7 3.4 - - - +
88A SER* 3.9 22.0 - - - +
90A LEU* 1.3 76.9 - - - +
92A ILE* 1.3 64.6 - - - +
93A ILE* 4.8 2.7 - - + -
123A VAL* 4.5 22.9 - - + +
127A SER* 4.4 4.9 - - - +
130A CYS* 3.9 23.3 - - + -
131A LYS 3.0 6.7 + - - +
132A ILE* 2.9 32.4 - - + +
133A ILE* 3.2 10.7 + - - +
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Residues in contact with ILE 92 (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 ILE* 4.8 1.8 - - + -
23A THR 3.1 18.7 + - - +
24A VAL* 3.4 22.5 - - + -
25A VAL 2.8 29.5 + - - +
31A GLY 4.9 0.9 - - - +
34A CYS* 3.2 26.2 - - - -
38A ILE* 4.9 6.7 - - + -
90A LEU* 4.1 19.5 - - + -
91A VAL* 1.3 77.0 - - - +
93A ILE* 1.3 56.2 + - - +
94A THR* 3.1 27.2 + - + +
133A ILE* 3.4 13.5 - - + +
135A VAL* 3.3 23.3 - - + -
255A VAL* 4.1 6.3 - - + -
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Residues in contact with ILE 93 (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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25A VAL* 4.1 9.0 - - + -
91A VAL* 4.8 8.3 - - + -
92A ILE* 1.3 67.4 - - - +
94A THR* 1.3 69.1 + - - +
95A ALA 3.8 2.0 - - - +
116A MET* 3.9 25.1 - - + -
119A ILE* 4.0 24.2 - - + -
120A VAL* 3.3 34.3 - - + -
123A VAL* 5.1 4.9 - - + -
132A ILE* 3.3 34.5 - - + -
133A ILE 3.4 5.5 + - - +
134A VAL* 4.2 15.3 - - + -
135A VAL 3.1 19.2 + - - -
136A THR* 3.4 7.2 + - + -
146A VAL* 4.4 0.9 - - + -
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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