Contacts of the helix formed by residues 502 - 515 (chain A) in PDB entry 1LWZ
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 THR 502 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98A LEU* 6.3 0.7 - - + -
364A LEU 3.0 13.8 + - - -
365A HIS 2.6 24.3 + - - +
366A GLY 3.2 15.7 - - - +
367A GLY* 3.4 3.3 + - - -
500A THR 3.6 4.3 + - - -
501A TRP* 1.3 70.8 - - - +
503A GLN* 1.3 59.5 + - - +
504A THR* 4.2 3.1 - - - -
505A TYR* 3.0 39.3 + - + +
506A LYS* 2.8 14.1 + - - +
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Residues in contact with GLN 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A LEU* 3.8 25.9 + - + +
365A HIS* 3.1 42.4 + - + +
497A PRO* 6.0 0.9 - - + -
501A TRP 3.7 0.8 + - - -
502A THR* 1.3 71.5 + - - +
504A THR* 1.3 61.6 + - - +
506A LYS* 2.7 36.6 - - + +
507A GLU* 3.2 7.7 + - - +
530A TYR* 5.0 4.8 - - - -
532A THR* 3.2 42.2 + - - +
536A VAL* 4.5 14.5 - - + +
538A PHE* 4.5 15.7 - - + -
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Residues in contact with THR 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A LEU* 4.2 2.0 - - + -
99A LYS* 2.7 52.2 - - + +
100A THR* 5.0 0.2 - - - -
365A HIS* 2.6 43.9 + - + -
366A GLY* 4.0 0.7 + - - -
502A THR* 4.2 4.0 - - - -
503A GLN* 1.3 77.7 - - - +
505A TYR* 1.3 62.1 + - - +
507A GLU* 2.7 42.5 - - + +
508A GLN* 2.8 7.9 + - + +
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Residues in contact with TYR 505 (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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1A LYS 4.4 8.5 + - - -
19A GLY 4.4 2.0 - - - -
20A ARG* 2.9 52.2 + - + +
98A LEU* 4.6 4.9 - - + -
501A TRP* 2.9 49.0 - + + +
502A THR* 3.0 26.9 + - + +
504A THR* 1.3 80.9 - - - +
506A LYS* 1.3 61.9 + - - +
508A GLN* 3.3 5.8 + - - +
509A VAL* 3.0 46.9 + - + +
560A LYS* 3.9 8.7 - - + +
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Residues in contact with LYS 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482A GLU* 4.9 1.8 - - - -
497A PRO* 3.3 31.7 - - - +
501A TRP* 2.7 56.2 + - - +
502A THR 2.8 12.3 + - - +
503A GLN* 2.7 33.6 - - + +
505A TYR* 1.3 77.9 - - - +
507A GLU* 1.3 59.4 + - - +
509A VAL* 2.7 15.3 - - + +
510A LEU* 2.7 31.4 + - + +
538A PHE* 3.1 34.3 - - + -
559A PHE 5.5 2.2 - - - +
560A LYS* 5.2 3.8 - - + -
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Residues in contact with GLU 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A GLU* 5.3 1.9 - - - +
100A THR* 5.9 0.5 - - - -
365A HIS* 2.9 39.5 + - - -
503A GLN* 3.2 5.6 + - - +
504A THR* 2.7 34.5 - - + +
506A LYS* 1.3 77.0 - - - +
508A GLN* 1.3 52.7 + - - +
510A LEU* 3.0 7.9 + - - +
511A GLU* 2.6 37.0 + - - +
530A TYR* 3.1 43.6 + - + +
538A PHE* 3.8 8.7 - - + -
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Residues in contact with GLN 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LYS* 4.0 6.4 + - - +
3A ASN* 3.3 25.4 + - - +
18A GLY 2.9 25.5 + - - -
19A GLY 3.3 17.6 - - - +
20A ARG* 4.9 0.2 - - - +
98A LEU* 3.5 35.9 - - + -
99A LYS 4.8 0.9 - - - +
100A THR 5.4 0.2 - - - +
504A THR 2.8 16.8 + - - +
505A TYR 3.5 4.2 - - - +
506A LYS 3.1 0.2 - - - -
507A GLU* 1.3 82.1 - - + +
509A VAL* 1.3 72.9 + - - +
511A GLU* 3.2 4.3 + - - -
512A PRO* 2.8 33.6 - - + +
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Residues in contact with VAL 509 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A LYS* 4.2 21.0 - - + +
505A TYR* 3.0 44.1 + - + +
506A LYS* 2.7 29.9 + - + +
508A GLN* 1.3 90.8 + - - +
510A LEU* 1.3 64.2 + - + +
512A PRO* 3.5 0.9 - - - +
513A MET* 3.1 28.6 + - - +
559A PHE* 6.5 0.2 - - + -
560A LYS* 3.0 42.0 - - + +
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Residues in contact with LEU 510 (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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506A LYS* 2.7 17.7 + - + +
507A GLU* 3.1 11.7 - - - +
509A VAL* 1.3 78.4 - - + +
511A GLU* 1.3 60.2 + - - +
513A MET* 4.4 6.1 - - - -
514A LEU* 2.6 87.5 + - + +
515A ASN* 3.1 1.3 + - - +
528A ARG* 2.9 55.6 - - + +
538A PHE* 4.3 12.1 - - + -
540A VAL* 5.3 1.3 - - + -
559A PHE* 4.6 12.1 - - + -
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Residues in contact with GLU 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A GLU 2.6 18.1 + - - +
508A GLN* 3.2 4.9 + - - +
510A LEU* 1.3 71.7 - - - +
512A PRO* 1.3 79.4 - - + +
515A ASN* 2.7 56.3 + - - +
516A GLY 3.3 1.6 - - - +
528A ARG* 2.8 26.7 + - - +
530A TYR* 4.2 2.1 + - - +
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Residues in contact with PRO 512 (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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1A LYS* 3.0 33.7 - - + +
3A ASN* 2.8 32.8 - - - +
508A GLN* 2.8 27.6 - - + +
510A LEU 3.4 0.2 - - - -
511A GLU* 1.3 92.5 - - + +
513A MET* 1.3 51.6 + - - +
515A ASN 2.6 17.2 - - - +
516A GLY 2.9 8.9 - - - +
517A THR* 2.6 29.3 + - - -
518A GLU* 4.4 1.1 - - - +
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Residues in contact with MET 513 (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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1A LYS* 4.3 9.1 - - + +
509A VAL 3.1 25.3 + - - +
510A LEU* 4.5 5.4 - - - -
512A PRO* 1.3 72.3 - - - +
514A LEU* 1.3 93.7 + - - +
515A ASN 3.0 4.4 + - - +
517A THR* 3.5 10.5 - - + -
522A PRO 5.8 0.4 - - - +
524A ILE* 2.7 66.7 + - + +
525A THR* 3.7 5.8 - - - +
558A VAL* 4.2 31.9 - - + +
559A PHE* 4.6 10.3 - - + -
560A LYS* 4.3 13.0 - - - +
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Residues in contact with LEU 514 (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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510A LEU* 2.6 59.4 + - + +
513A MET* 1.3 76.5 - - - +
515A ASN* 1.3 60.9 + - + +
525A THR* 2.5 75.2 - - + +
526A ASP 4.2 0.3 - - - -
527A TYR* 3.0 15.5 - - - -
528A ARG* 3.0 23.3 - - + +
540A VAL* 2.9 21.3 - - + -
559A PHE* 4.1 7.0 - - + -
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Residues in contact with ASN 515 (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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510A LEU* 3.1 3.8 + - - +
511A GLU* 2.7 68.3 + - - +
512A PRO 2.6 16.3 - - - +
513A MET 3.0 1.3 - - - +
514A LEU* 1.3 87.8 - - + +
516A GLY* 1.3 75.9 + - - +
517A THR* 2.8 5.0 + - - -
523A LEU* 3.1 19.1 - - - +
525A THR 4.0 3.1 - - - -
526A ASP 5.2 4.9 - - - +
527A TYR* 5.6 2.9 - - + -
528A ARG* 3.7 13.9 - - - +
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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