Contacts of the strand formed by residues 121 - 123 (chain A) in PDB entry 3LKB
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 LEU 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A PRO* 3.9 24.5 - - + -
105A SER 3.9 14.8 - - - +
106A MET* 4.4 9.4 - - - +
107A HIS 3.8 21.3 - - - +
108A ILE* 4.4 7.9 - - + -
110A LEU* 4.5 7.0 - - + -
111A ILE* 3.8 35.2 - - + -
119A ILE* 4.2 3.1 + - + -
120A PHE* 1.3 70.7 - - - +
122A PRO* 1.3 59.3 - - + +
123A THR 3.8 17.5 - - - +
125A SER* 4.7 3.4 - - - -
345A PHE* 3.3 5.1 - - - -
350A HIS 2.9 11.8 + - - +
351A THR* 4.3 6.7 - - - +
352A GLY 2.7 32.1 + - - -
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Residues in contact with PRO 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TYR* 5.4 0.7 - - - +
102A ILE* 3.4 24.5 - - + -
103A PRO 3.4 22.9 - - - +
105A SER 5.3 0.7 - - - +
106A MET* 6.1 3.4 - - + -
120A PHE 3.6 5.6 - - - +
121A LEU* 1.3 84.6 - - + +
123A THR* 1.3 65.4 + - + +
289A ASN* 5.5 7.2 - - - +
292A LEU* 3.9 22.0 - - + -
293A ALA* 4.8 8.3 - - + +
296A ILE* 4.0 16.4 - - + -
343A ILE* 4.0 5.4 - - - +
345A PHE* 4.5 2.2 - - + -
352A GLY* 3.4 3.0 - - - +
353A ALA* 2.9 23.4 + - - +
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Residues in contact with THR 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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106A MET* 3.6 24.3 - - + +
121A LEU* 3.8 14.4 - - - +
122A PRO* 1.3 88.5 - - + +
124A THR* 1.3 75.2 + - - +
129A GLN* 4.5 0.9 + - - -
254A SER* 3.6 23.0 + - - -
255A PHE* 3.6 33.2 - - + -
289A ASN* 5.5 0.2 - - - +
292A LEU* 3.9 9.9 - - + -
334A ALA* 4.6 0.9 - - + -
351A THR* 3.6 12.9 - - - +
353A ALA* 3.6 13.7 - - + +
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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