Contacts of the strand formed by residues 28 - 32 (chain A) in PDB entry 1L2L
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 VAL 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A VAL* 3.9 18.8 - - + -
27A GLY* 1.3 76.7 - - - +
29A LEU* 1.3 65.3 + - - +
30A LEU* 3.4 25.5 + - + -
124A LEU* 4.1 13.2 - - + -
130A ILE* 3.9 13.0 - - + -
131A PRO 2.8 12.2 + - - +
132A VAL* 3.5 9.1 - - + +
133A ILE* 3.0 23.5 + - - +
229A SER* 4.3 1.6 - - - -
231A LEU* 3.3 14.4 - - + +
233A ILE* 4.0 16.6 - - + -
451A VAL* 4.2 18.2 - - + -
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Residues in contact with LEU 29 (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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28A VAL* 1.3 72.0 - - - +
30A LEU* 1.3 59.6 + - - +
31A ALA* 5.1 3.6 - - + -
133A ILE* 3.6 22.7 - - + +
218A TRP* 3.3 34.5 - - + -
222A PHE* 3.6 34.8 - - + -
225A ILE* 4.1 11.2 - - + +
226A ALA* 4.5 7.6 - - - -
229A SER* 3.8 12.2 - - - +
231A LEU 2.8 15.9 + - - +
232A ALA* 3.2 9.1 - - + +
233A ILE 2.8 32.6 + - - +
234A ILE* 5.5 2.9 - - + +
259A LEU* 4.1 15.3 - - + -
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Residues in contact with LEU 30 (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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28A VAL* 3.4 25.1 + - + +
29A LEU* 1.3 80.2 - - - +
31A ALA* 1.3 62.4 + - - +
116A GLN 5.0 0.2 - - - +
117A VAL* 3.5 27.2 - - + +
120A MET* 3.8 13.2 - - + +
121A ALA* 3.4 27.6 - - + +
124A LEU* 4.3 6.3 - - + -
132A VAL* 3.4 28.5 - - + -
133A ILE 3.0 12.0 + - - +
134A ALA* 4.5 0.2 - - - -
135A HIS* 3.0 24.3 + - - +
218A TRP* 4.1 1.4 - - - -
233A ILE* 3.5 20.6 - - + +
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Residues in contact with ALA 31 (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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29A LEU* 4.2 4.0 - - + -
30A LEU* 1.3 74.7 - - - +
32A TYR* 1.3 96.7 + - + +
117A VAL* 3.3 15.0 - - - +
135A HIS* 3.7 1.3 - - + -
218A TRP* 4.0 19.7 - - + -
222A PHE* 5.7 1.1 - - + -
233A ILE 3.4 10.7 + - - -
234A ILE* 4.0 11.6 - - + +
235A SER 3.1 20.6 + - - +
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Residues in contact with TYR 32 (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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31A ALA* 1.3 94.3 - - + +
33A ASN* 1.3 61.1 + - - +
117A VAL* 3.7 2.0 - - - +
135A HIS* 3.0 38.6 + + - +
137A PRO* 3.2 20.6 - - - +
209A ASN* 4.2 1.1 - - - -
212A LEU* 3.5 30.7 - - + -
213A TYR 4.6 3.4 - - - +
214A VAL* 3.7 32.5 - - + -
218A TRP* 5.2 2.0 - + - -
222A PHE* 5.0 0.5 - - - -
234A ILE* 3.6 29.7 - - + +
235A SER 3.7 9.4 - - - +
237A LEU* 5.0 0.4 - - + -
252A VAL* 3.7 25.1 - - + +
255A HIS* 2.7 41.5 - + - +
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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