Contacts of the strand formed by residues 412 - 418 (chain A) in PDB entry 3LPJ
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 ARG 412 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A TYR* 3.5 47.0 + - + -
252A THR 3.3 13.9 - - - +
253A PRO* 4.5 0.7 - - + -
254A ILE* 3.6 5.6 - - - +
351A GLU* 2.8 48.8 + - - +
407A ASP* 2.9 58.2 + - + +
410A ARG* 3.2 55.2 - - - +
411A LYS* 1.3 79.0 - - - +
413A ILE* 1.3 65.5 + - - +
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Residues in contact with ILE 413 (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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250A TRP 3.8 0.7 - - - +
251A TYR* 3.3 3.0 - - - -
252A THR* 2.8 43.5 + - + +
254A ILE* 3.7 17.9 - - + -
260A TYR* 3.8 29.6 - - + +
262A VAL* 3.7 24.5 - - + -
288A VAL* 4.0 8.7 - - + -
404A VAL* 3.7 19.7 - - + -
405A VAL 3.2 11.0 - - - +
406A PHE* 4.5 11.0 - - + -
412A ARG* 1.3 79.0 - - - +
414A GLY* 1.3 62.3 + - - +
415A PHE* 3.6 24.1 - - + -
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Residues in contact with GLY 414 (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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249A LEU* 4.1 6.7 - - - -
250A TRP 3.2 8.5 - - - -
251A TYR* 3.3 23.4 - - - -
404A VAL* 3.3 7.6 - - - +
405A VAL* 2.8 39.2 + - - -
413A ILE* 1.3 74.3 - - - +
415A PHE* 1.3 64.6 + - - -
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Residues in contact with PHE 415 (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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249A LEU* 3.4 4.2 - - - +
250A TRP 2.8 33.7 + - - +
252A THR* 4.2 8.3 - - + -
262A VAL* 5.5 0.4 - - + -
288A VAL* 4.3 13.7 - - + -
348A LEU* 3.7 22.9 - - + -
357A PHE* 4.2 7.0 - + + -
359A ILE* 4.0 29.2 - - + -
394A MET* 3.9 29.6 - - + -
398A ILE* 5.9 0.7 - - + -
399A MET* 6.1 2.2 - - + -
402A PHE* 4.2 13.7 - + + -
403A TYR 3.5 3.1 - - - -
404A VAL* 4.1 25.6 - - + -
413A ILE* 3.6 29.8 - - + -
414A GLY* 1.3 76.2 - - - -
416A ALA* 1.3 60.1 + - - +
431A VAL* 3.4 13.8 - - + +
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Residues in contact with ALA 416 (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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245A TYR* 3.4 37.2 - - + -
246A THR 4.2 0.2 - - - +
248A SER 3.6 14.1 - - - +
249A LEU* 3.5 15.7 - - + -
402A PHE* 3.2 6.4 - - - +
403A TYR 2.9 30.7 + - - +
415A PHE* 1.3 75.1 - - - +
417A VAL* 1.3 61.3 + - - +
431A VAL* 3.7 8.5 - - - -
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Residues in contact with VAL 417 (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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245A TYR* 3.2 6.4 - - - +
246A THR* 3.1 48.9 + - - +
247A GLY* 6.1 0.9 - - - -
248A SER 4.9 0.2 + - - -
401A GLY 4.0 6.3 - - - +
402A PHE* 4.2 2.5 - - + -
416A ALA* 1.3 71.5 - - - +
418A SER* 1.3 64.5 + - - +
421A HIS* 3.4 30.7 - - + +
428A THR* 4.5 1.3 - - - +
429A ALA* 3.7 8.7 - - + +
430A ALA* 3.5 34.3 - - - +
431A VAL* 3.6 11.5 - - + +
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Residues in contact with SER 418 (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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214A GLN* 3.8 9.4 - - - +
215A LEU 4.9 0.2 + - - -
244A LEU 3.9 4.7 - - - -
246A THR* 5.1 1.0 + - - +
400A GLU 4.1 4.2 + - - -
401A GLY 3.0 31.5 + - - -
402A PHE 3.6 13.0 + - - -
403A TYR 4.0 3.8 - - - +
416A ALA 3.3 1.8 + - - -
417A VAL* 1.3 74.5 - - - +
419A ALA* 1.3 62.7 + - - +
420A CYS* 3.0 31.7 + - - -
421A HIS* 2.9 30.0 + - - -
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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