Contacts of the helix formed by residues 298 - 309 (chain A) in PDB entry 2LBP
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 GLU 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A SER* 3.5 18.9 + - - +
297A ASP* 1.3 71.9 - - - +
299A PRO* 1.3 74.1 - - + +
300A LEU* 3.1 13.5 + - + +
301A ALA* 3.1 24.7 + - + +
302A LEU* 3.5 12.8 + - - +
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Residues in contact with PRO 299 (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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71A LYS* 3.8 33.4 - - + +
72A TYR* 4.4 1.1 - - + -
93A GLY 3.3 26.7 - - - +
95A LEU* 3.9 26.2 - - + +
113A HIS* 4.0 10.7 - - + +
297A ASP 3.5 5.8 - - - +
298A GLU* 1.3 86.4 - - + +
300A LEU* 1.3 56.8 + - - +
302A LEU* 2.9 28.8 - - + +
303A VAL* 3.4 9.7 + - - +
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Residues in contact with LEU 300 (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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112A GLN* 4.2 24.9 - - + +
113A HIS* 3.7 33.2 - - + +
298A GLU* 3.1 11.8 + - - +
299A PRO* 1.3 75.8 - - - +
301A ALA* 1.3 62.0 + - - +
302A LEU 3.1 1.6 - - - -
303A VAL* 3.1 14.0 - - + +
304A LYS* 3.0 60.8 - - - +
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Residues in contact with ALA 301 (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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291A LEU* 3.3 11.4 - - - +
294A THR* 5.1 2.1 + - + -
296A SER* 3.4 28.0 - - - +
298A GLU* 3.1 19.3 + - + +
300A LEU* 1.3 78.4 - - - +
302A LEU* 1.3 54.9 + - - +
304A LYS* 3.4 15.1 + - - +
305A ASP* 3.3 17.7 + - - +
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Residues in contact with LEU 302 (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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72A TYR* 3.4 36.3 - - + -
95A LEU* 3.7 18.8 - - + -
115A MET* 4.6 0.2 - - - -
287A LEU* 3.8 17.3 - - + +
291A LEU* 2.4 72.7 - - + +
292A GLU* 4.3 7.2 - - + -
296A SER 5.0 0.7 - - - +
297A ASP 4.1 5.2 - - - +
298A GLU 3.6 12.8 - - - +
299A PRO* 2.9 19.1 - - + +
301A ALA* 1.3 69.6 - - - +
303A VAL* 1.3 59.9 + - - +
304A LYS 3.2 0.4 - - - -
306A LEU* 3.3 20.7 + - + +
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Residues in contact with VAL 303 (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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95A LEU* 4.4 5.6 - - + -
112A GLN 3.3 21.8 - - - +
113A HIS* 4.9 2.9 - - - -
115A MET* 3.4 32.3 - - + +
299A PRO 4.0 4.0 - - - +
300A LEU* 3.1 31.6 - - + +
302A LEU* 1.3 78.4 - - - +
304A LYS* 1.3 63.6 + - + +
306A LEU* 4.2 0.5 - - - +
307A LYS* 2.9 61.1 + - + +
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Residues in contact with LYS 304 (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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300A LEU* 3.0 53.3 + - + +
301A ALA* 3.4 11.5 + - - +
302A LEU 3.2 0.8 - - - -
303A VAL* 1.3 83.6 - - + +
305A ASP* 1.3 52.4 + - - +
307A LYS* 3.6 5.2 - - - +
308A ALA* 2.8 35.4 + - - +
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Residues in contact with ASP 305 (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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290A ALA* 5.5 0.2 - - - -
291A LEU* 3.0 47.6 + - + +
294A THR* 3.7 18.5 + - - +
301A ALA 3.3 4.3 + - - +
302A LEU 3.7 0.2 + - - -
304A LYS* 1.3 76.1 - - - +
306A LEU* 1.3 59.2 + - - +
308A ALA* 4.5 0.7 - - - -
309A ASN* 2.9 59.2 + - - +
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Residues in contact with LEU 306 (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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97A ILE* 4.8 2.9 - - + -
115A MET* 3.7 29.8 - - + -
286A SER* 3.0 37.0 - - - +
287A LEU* 4.2 6.3 - - - +
290A ALA* 3.7 26.2 - - + -
291A LEU* 4.1 9.0 - - + +
302A LEU* 3.3 17.5 + - + +
304A LYS 3.5 0.2 - - - -
305A ASP* 1.3 78.9 - - - +
307A LYS* 1.3 60.3 + - - +
309A ASN 2.3 24.5 - - - +
310A GLY 4.3 7.9 - - - +
320A TRP* 3.3 38.9 + - + +
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Residues in contact with LYS 307 (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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111A TYR 4.9 2.0 + - - -
112A GLN* 3.9 18.9 + - - +
114A ILE 4.7 4.0 + - - -
115A MET* 4.8 5.3 - - - -
303A VAL* 2.9 48.8 + - + +
304A LYS* 4.1 5.6 - - - +
306A LEU* 1.3 80.1 - - - +
308A ALA* 1.3 58.4 + - - +
309A ASN 4.2 0.7 - - - +
319A ASN* 4.4 5.9 + - - -
320A TRP* 4.1 18.7 - - + +
321A ASP 3.6 19.1 - - - +
322A GLU* 3.1 35.4 + - - +
323A LYS 4.4 2.4 + - - -
324A GLY* 4.1 14.4 - - - +
327A LYS* 5.2 0.7 + - - -
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Residues in contact with ALA 308 (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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304A LYS 2.8 19.1 + - - +
305A ASP* 4.5 0.4 - - - -
306A LEU 3.2 0.2 - - - -
307A LYS* 1.3 79.4 - - - +
309A ASN* 1.3 75.2 + - - +
319A ASN* 5.8 1.2 + - - -
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Residues in contact with ASN 309 (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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305A ASP* 2.9 37.4 + - - +
306A LEU 2.3 32.0 - - - +
307A LYS 3.9 0.9 - - - +
308A ALA* 1.3 88.1 - - - +
310A GLY* 1.3 60.9 + - - +
319A ASN* 4.7 5.5 + - - -
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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