Contacts of the helix formed by residues 512 - 527 (chain K) in PDB entry 5G04
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 ASP 512 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1323A GLU* 5.4 0.4 - - - -
479K ALA* 5.1 5.7 - - - +
480K SER* 5.3 2.5 - - - -
483K SER* 4.1 11.3 + - - -
505K ALA* 5.7 0.8 - - - +
506K LEU* 3.8 0.4 - - + +
509K ARG* 3.5 40.1 + - + +
510K ARG 3.2 6.1 + - - -
511K ASP* 1.3 75.1 - - - +
513K THR* 1.3 61.8 + - - +
514K PHE* 4.7 6.7 + - - +
515K SER* 2.8 28.7 + - - +
516K VAL* 2.9 32.9 + - - +
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Residues in contact with THR 513 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1320A ASN* 4.2 6.4 + - - -
1323A GLU* 2.7 66.8 + - + +
1326A TYR* 5.4 9.4 - - + -
1327A GLN* 5.8 5.2 - - + +
511K ASP* 4.0 4.2 + - - +
512K ASP* 1.3 71.5 + - - +
514K PHE* 1.3 57.9 + - - +
516K VAL* 3.6 9.3 - - + +
517K THR* 2.7 40.2 + - - +
13W LEU* 5.5 4.8 - - - +
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Residues in contact with PHE 514 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483K SER* 3.9 22.7 - - - -
487K TYR* 3.6 21.5 - + + -
502K PHE* 4.2 6.7 - + - -
512K ASP* 3.4 8.3 + - - +
513K THR* 1.3 76.8 + - - +
515K SER* 1.3 69.7 + - - +
517K THR* 3.4 8.0 - - - +
518K MET* 2.9 51.7 + - + +
11W LEU* 3.5 62.4 - - + +
12W LYS* 4.2 8.7 - - - -
13W LEU* 5.3 8.3 - - + +
16W ILE* 3.7 23.3 - - + -
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Residues in contact with SER 515 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483K SER* 3.7 24.3 - - - -
502K PHE* 3.7 15.8 - - - +
505K ALA* 4.6 7.1 - - - +
506K LEU* 3.3 17.3 - - - +
512K ASP* 2.8 34.5 + - - +
514K PHE* 1.3 84.4 - - - +
516K VAL* 1.3 56.0 + - - +
518K MET* 3.7 1.0 - - - +
519K LEU* 2.9 30.7 + - - +
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Residues in contact with VAL 516 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1326A TYR* 5.9 7.0 - - + -
506K LEU* 3.6 31.2 - - + +
510K ARG 4.4 9.9 - - - +
512K ASP 2.9 25.6 + - - +
513K THR* 3.2 10.1 + - + +
515K SER* 1.3 75.7 - - - +
517K THR* 1.3 63.7 + - - +
519K LEU* 3.2 14.2 + - + +
520K GLY* 3.2 9.7 + - - -
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Residues in contact with THR 517 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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513K THR* 2.7 30.9 + - - +
514K PHE* 3.4 8.5 - - - +
516K VAL* 1.3 73.1 - - - +
518K MET* 1.3 66.6 + - - +
520K GLY* 3.0 14.1 + - - -
521K HIS* 3.3 30.0 + - - -
13W LEU* 5.0 4.9 - - + -
16W ILE* 3.4 29.4 - - + +
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Residues in contact with MET 518 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487K TYR* 3.3 34.5 - - + -
490K SER* 4.6 5.2 - - - -
502K PHE* 3.3 34.3 - - + -
514K PHE* 2.9 24.9 + - + +
515K SER 3.7 3.1 - - - +
517K THR* 1.3 78.1 - - - +
519K LEU* 1.3 63.0 + - - +
521K HIS* 3.6 4.5 + - - +
522K CYS* 3.3 24.0 + - - -
16W ILE* 3.5 44.9 - - + -
19W PHE* 4.1 24.9 - - + -
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Residues in contact with LEU 519 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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625H ARG* 4.2 3.4 - - - +
645H TYR* 5.0 4.3 - - - +
499K VAL* 4.0 22.2 - - + +
502K PHE* 3.9 26.5 - - + +
503K HIS* 3.8 23.1 - - + +
506K LEU* 3.7 25.6 - - + -
515K SER 2.9 18.3 + - - +
516K VAL* 3.3 8.1 - - + +
517K THR 3.0 0.2 - - - -
518K MET* 1.3 75.1 - - - +
520K GLY* 1.3 67.0 + - - +
522K CYS* 3.1 5.0 + - - +
523K ILE* 3.1 39.6 + - + +
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Residues in contact with GLY 520 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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516K VAL 3.2 6.4 + - - -
517K THR 3.0 9.2 + - - -
519K LEU* 1.3 79.5 - - - +
521K HIS* 1.3 61.1 + - - +
523K ILE* 3.3 8.4 + - - +
524K GLU* 3.1 28.7 + - - +
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Residues in contact with HIS 521 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517K THR* 3.3 35.2 + - - -
518K MET* 3.9 9.5 - - - +
519K LEU 3.3 0.6 - - - -
520K GLY* 1.3 73.9 - - - +
522K CYS* 1.3 64.6 + - - +
524K GLU* 3.3 16.2 + - - -
525K MET* 3.0 7.4 + - - +
16W ILE* 4.9 12.3 - - + +
19W PHE* 3.8 21.8 - + + -
20W GLU* 3.6 27.1 + - - -
23W ARG* 3.0 34.5 + - - +
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Residues in contact with CYS 522 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490K SER* 3.3 34.8 - - - -
495K PHE* 4.0 23.8 - - + +
498K ALA* 4.7 2.9 - - + -
499K VAL* 4.0 16.8 - - + +
502K PHE* 4.5 12.8 - - + -
518K MET* 3.3 16.3 + - - +
519K LEU* 3.1 9.9 + - - +
521K HIS* 1.3 78.8 - - - +
523K ILE* 1.3 58.3 + - - +
525K MET* 3.4 3.0 + - - +
526K TYR* 2.8 29.6 + - - +
19W PHE* 4.3 6.7 - - - -
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Residues in contact with ILE 523 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653H LEU* 3.1 36.8 - - + -
656H MET* 3.5 30.5 - - + +
657H HIS* 4.1 16.4 - - + +
660H LYS* 3.7 6.7 - - - +
499K VAL* 3.5 28.9 - - + -
503K HIS* 4.6 0.9 - - + +
519K LEU* 3.1 31.1 + - + +
520K GLY* 3.7 6.3 - - - +
521K HIS 3.2 0.2 - - - -
522K CYS* 1.3 75.5 - - - +
524K GLU* 1.3 64.9 + - - +
526K TYR* 3.2 7.5 + - - +
527K ILE* 3.1 28.9 + - + +
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Residues in contact with GLU 524 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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653H LEU* 5.8 3.1 - - + -
520K GLY 3.1 15.3 + - - +
521K HIS* 3.3 17.4 + - - +
523K ILE* 1.3 79.2 - - + +
525K MET* 1.3 59.8 + - - +
527K ILE* 3.5 29.2 + - + +
23W ARG* 3.4 21.9 + - - +
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Residues in contact with MET 525 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495K PHE* 3.4 49.0 - - + -
521K HIS 3.0 14.6 + - - +
522K CYS 3.5 7.9 - - - +
524K GLU* 1.3 73.7 - - - +
526K TYR* 1.3 63.6 + - - +
527K ILE 3.4 5.9 + - - +
19W PHE* 5.2 0.4 - - + -
22W ILE* 5.4 4.5 - - + +
23W ARG* 3.2 45.4 - - + +
25W ASP 6.2 1.6 - - - +
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Residues in contact with TYR 526 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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656H MET* 3.1 44.0 - - + -
659H GLN* 5.9 6.5 - - + +
660H LYS* 4.3 18.0 - - + +
663H ASP* 5.7 1.2 + - - -
495K PHE* 3.9 10.5 - - + +
496K GLU* 3.3 58.0 - - + +
499K VAL* 5.0 2.9 - - + -
522K CYS 2.8 21.3 + - - +
523K ILE* 3.2 6.0 + - - +
525K MET* 1.3 72.7 - - - +
527K ILE* 1.3 60.8 + - - +
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Residues in contact with ILE 527 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652H SER* 3.9 38.4 - - - +
653H LEU* 4.7 2.9 - - + -
656H MET* 3.6 20.9 - - + -
684H LYS* 5.8 6.1 - - - +
523K ILE* 3.1 27.6 + - + +
524K GLU* 3.6 21.4 - - + +
525K MET 3.3 6.7 - - - +
526K TYR* 1.3 80.9 - - - +
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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