Contacts of the helix formed by residues 122 - 127 (chain B) 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 GLY 122 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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82B TYR* 4.4 7.0 - - - -
118B ALA 5.3 0.9 - - - -
119B ILE 5.0 0.4 - - - -
120B VAL 3.6 0.2 - - - -
121B PRO* 1.3 73.2 - - - +
123B VAL* 1.3 56.0 + - - +
124B ILE* 3.0 5.6 - - - +
125B GLN* 2.9 26.5 + - - +
126B ASN* 2.5 29.9 + - - -
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Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B VAL* 4.4 11.0 - - + -
82B TYR* 3.2 31.2 - - + +
85B SER* 5.1 6.1 - - - +
91B VAL* 4.5 25.7 - - + +
93B ILE* 5.1 4.5 - - + -
119B ILE* 2.8 33.6 + - + +
120B VAL* 2.8 20.0 + - + +
122B GLY* 1.3 73.5 - - - +
124B ILE* 1.3 75.4 + - + +
126B ASN* 3.2 19.3 + - - +
127B SER* 3.3 14.6 + - - -
130B CYS* 5.6 1.7 - - - +
132B ILE* 5.3 4.9 - - + -
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Residues in contact with ILE 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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121B PRO* 3.2 41.5 - - + -
122B GLY 4.9 0.2 - - - +
123B VAL* 1.3 84.8 - - + +
125B GLN* 1.3 67.7 + - + +
126B ASN 2.9 2.8 + - - -
127B SER 4.3 5.8 - - - -
128B PRO* 3.1 29.6 - - + +
130B CYS* 5.2 1.8 - - - -
132B ILE* 5.1 2.0 - - + -
150B SER* 3.6 34.8 - - - +
152B PHE* 3.3 40.6 - - + -
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Residues in contact with GLN 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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122B GLY* 2.9 23.6 + - - +
124B ILE* 1.3 82.5 - - - +
126B ASN* 1.3 65.2 + - - +
128B PRO* 4.6 5.5 - - - +
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Residues in contact with ASN 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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82B TYR* 3.2 42.2 - - - +
83B ASN* 3.4 21.8 + - - +
85B SER* 4.7 0.7 - - - -
86B ALA* 4.5 15.1 - - - +
87B ASN* 4.6 8.8 + - - +
122B GLY 2.5 30.3 + - - -
123B VAL 3.3 6.4 + - - +
124B ILE 2.9 1.0 - - - -
125B GLN* 1.3 84.5 - - - +
127B SER* 1.3 60.0 - - - +
128B PRO* 2.8 13.9 - - - +
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Residues in contact with SER 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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85B SER* 3.0 22.3 + - - -
87B ASN* 3.7 6.7 - - - +
88B SER* 3.2 39.5 + - - -
91B VAL* 4.4 4.2 - - - +
123B VAL 3.3 8.7 + - - -
124B ILE* 3.2 7.5 - - - +
126B ASN* 1.3 72.0 - - - +
128B PRO* 1.3 61.2 - - - +
129B ASP 3.2 2.0 - - - -
130B CYS* 2.8 40.4 + - - +
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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