Contacts of the strand formed by residues 519 - 525 (chain A) in PDB entry 1L7R
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 519 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431A SER* 4.3 15.9 + - - -
432A THR* 2.9 35.7 + - - +
433A GLU* 3.8 9.1 - - - +
434A VAL* 3.6 34.2 - - + +
435A LEU* 4.6 1.3 - - - -
466A ASP* 3.8 5.2 - - - +
467A VAL* 3.0 51.9 + - + +
514A PHE* 3.8 5.1 - - - -
517A GLY 5.3 1.1 - - - +
518A HIS* 1.3 80.3 - - - +
520A ILE* 1.3 65.6 + - - +
521A MET 3.8 0.3 + - - -
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Residues in contact with ILE 520 (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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361A PHE* 4.3 20.0 - - + -
378A LEU* 3.5 14.1 - - + +
431A SER* 3.3 2.6 - - - -
432A THR* 2.9 42.9 + - + +
435A LEU* 4.2 9.4 - - + +
439A VAL* 4.0 30.7 - - + -
464A LEU* 3.9 23.8 - - + -
465A VAL 3.9 2.9 - - - -
514A PHE* 3.6 32.1 - - + -
519A ARG* 1.3 72.3 - - - +
521A MET* 1.3 61.2 + - - +
569A LEU* 4.1 17.9 - - + -
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Residues in contact with MET 521 (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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372A SER* 4.4 5.6 - - - -
422A HIS* 3.5 31.6 - - + +
429A CYS* 3.2 41.5 - - + -
430A TYR 3.3 6.1 - - - +
431A SER* 3.2 20.6 - - - +
464A LEU* 3.6 2.4 - - - +
465A VAL* 2.7 51.0 + - + +
467A VAL* 3.7 30.3 - - + -
520A ILE* 1.3 74.9 - - - +
522A VAL* 1.3 75.4 + - - +
523A GLN* 4.4 5.2 - - + +
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Residues in contact with VAL 522 (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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363A LEU* 5.7 3.8 - - + -
378A LEU* 3.7 23.3 - - + -
428A LEU 3.6 1.0 - - - +
429A CYS* 3.5 3.3 - - - -
430A TYR* 2.8 40.9 + - + +
462A ALA* 4.7 6.7 - - + -
463A LYS 3.2 12.8 - - - +
464A LEU* 4.2 4.9 - - + -
521A MET* 1.3 81.7 - - - +
523A GLN* 1.3 75.1 + - - +
524A VAL* 4.0 14.6 - - + -
567A ILE* 3.7 39.0 - - + -
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Residues in contact with GLN 523 (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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399A VAL* 5.7 1.0 - - - +
418A GLN* 3.3 31.3 + - - +
421A ILE* 4.2 7.3 - - - +
422A HIS* 3.4 12.1 + - - -
427A VAL* 4.0 25.1 - - + +
428A LEU 3.2 6.1 - - - +
429A CYS* 4.5 0.9 - - - -
461A THR* 4.3 0.7 + - - -
462A ALA* 3.2 4.9 - - - -
463A LYS* 2.9 71.8 + - + +
465A VAL* 4.1 11.3 - - + +
521A MET* 4.4 13.7 - - + -
522A VAL* 1.3 76.7 - - - +
524A VAL* 1.3 62.3 + - - +
525A SER* 6.3 0.4 - - - -
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Residues in contact with VAL 524 (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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363A LEU* 4.5 8.7 - - + -
391A TYR* 4.7 0.9 - - - +
426A ASP 3.7 0.9 - - - +
427A VAL* 3.8 0.7 - - - -
428A LEU* 2.8 47.0 + - + +
430A TYR* 3.9 18.8 - - + -
449A LEU* 4.0 20.0 - - + -
460A PHE* 5.0 1.1 - - + -
461A THR 3.3 13.0 - - - +
462A ALA* 4.8 2.2 - - + -
522A VAL* 4.0 14.4 - - + -
523A GLN* 1.3 79.6 - - - +
525A SER* 1.3 70.5 + - - +
557A ILE* 3.8 32.5 - - + -
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Residues in contact with SER 525 (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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391A TYR* 3.1 18.6 + - - -
399A VAL* 3.4 26.2 - - - +
426A ASP* 2.6 28.1 + - - +
427A VAL* 4.5 6.1 - - - -
460A PHE* 3.2 7.1 - - - -
461A THR* 2.7 41.6 + - - +
523A GLN* 6.3 0.4 - - - -
524A VAL* 1.3 75.5 - - - +
526A SER* 1.3 62.0 + - - +
527A SER* 4.0 3.0 + - - -
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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