Contacts of the strand formed by residues 525 - 531 (chain B) in PDB entry 1LJ1
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 525 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513B ASP* 3.6 24.2 - - - +
517B GLU* 3.7 29.4 - - + +
518B VAL 3.6 5.2 - - - -
519B MET* 4.4 11.4 - - + +
520B ASN* 5.6 0.2 + - - -
523B LYS 4.2 0.2 + - - -
524B GLN* 1.3 81.1 - - - +
526B ILE* 1.3 73.7 + - - +
527B PRO* 3.4 19.8 - - + +
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Residues in contact with ILE 526 (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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283B LYS* 4.3 19.7 - - + +
287B GLY 4.1 14.6 - - - +
289B VAL* 4.9 1.8 - - + -
352B ALA 3.8 7.4 - - - +
353B GLY* 3.6 35.4 - - - +
354B GLY* 3.7 4.3 - - - +
518B VAL* 3.0 25.8 + - + +
520B ASN* 4.3 11.9 - - + +
524B GLN 4.4 4.7 - - - +
525B VAL* 1.3 77.8 - - - +
527B PRO* 1.3 70.2 - - - +
528B GLY 3.4 0.5 + - - -
529B LEU* 3.3 41.1 + - + +
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Residues in contact with PRO 527 (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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286B LYS 5.7 0.4 - - - +
287B GLY 3.9 16.4 - - - +
288B THR* 3.6 20.1 - - + -
289B VAL* 3.0 29.1 + - - +
525B VAL* 3.4 20.0 - - + +
526B ILE* 1.3 83.4 - - - +
528B GLY* 1.3 58.8 + - - +
567B TYR* 3.6 22.4 - - + +
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Residues in contact with GLY 528 (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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289B VAL* 3.6 5.8 - - - +
307B ASP 3.8 8.3 - - - -
308B ALA* 3.2 6.5 - - - +
309B VAL 2.9 28.1 + - - +
526B ILE 3.4 0.6 + - - -
527B PRO* 1.3 71.2 - - - +
529B LEU* 1.3 57.3 + - - +
530B TYR* 3.7 12.7 + - - -
567B TYR* 3.5 33.4 - - - -
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Residues in contact with LEU 529 (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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281B VAL* 4.1 27.8 - - + -
289B VAL* 3.9 9.9 - - + -
309B VAL* 3.5 14.4 - - + +
311B LEU* 4.3 21.3 - - + -
349B ALA* 4.9 2.5 - - - +
352B ALA* 3.8 26.5 - - + -
517B GLU* 3.8 3.6 - - - +
518B VAL* 3.1 49.4 + - + -
526B ILE* 3.3 31.5 + - + +
527B PRO 3.4 1.2 + - - -
528B GLY* 1.3 76.3 - - - +
530B TYR* 1.3 62.5 + - - +
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Residues in contact with TYR 530 (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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308B ALA* 4.2 3.6 - - + -
309B VAL 2.9 13.6 + - - +
310B ILE* 4.0 15.7 - - + -
311B LEU* 3.1 28.3 + - - +
515B LYS 3.8 3.4 - - - -
516B ALA* 3.2 25.1 - - + +
517B GLU* 3.7 29.4 + - + -
518B VAL* 3.7 8.2 - - - +
528B GLY* 3.7 27.4 + - - -
529B LEU* 1.3 75.2 - - - +
531B GLY* 1.3 57.8 + - - +
560B ALA* 4.1 13.7 - - + -
563B GLU* 3.6 25.1 + - + +
564B ALA* 3.9 27.8 - - + -
567B TYR* 3.4 28.6 - - + +
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Residues in contact with GLY 531 (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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310B ILE* 5.1 0.2 - - - -
311B LEU* 3.3 11.7 - - - -
510B VAL* 4.8 5.6 - - - -
512B ILE* 3.7 12.6 - - - +
516B ALA* 3.1 26.0 + - - +
518B VAL* 3.8 8.1 - - - +
530B TYR* 1.3 73.5 - - - +
532B ALA* 1.3 64.2 + - - +
535B VAL* 4.8 0.2 - - - -
536B THR* 3.6 15.9 - - - +
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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