Contacts of the helix formed by residues 511 - 522 (chain A) in PDB entry 4HPF
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 GLN 511 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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509A PRO* 4.3 2.3 - - - +
510A LYS* 1.3 92.7 - - + +
512A THR* 1.3 65.9 + - - +
513A TRP* 3.1 35.6 + - + +
514A LYS* 3.2 19.3 + - + +
515A LYS* 3.0 21.8 + - - +
1006A GLU* 4.2 19.0 - - - +
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Residues in contact with THR 512 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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511A GLN* 1.3 72.7 - - - +
513A TRP* 1.3 64.9 + - - +
515A LYS* 3.0 23.0 + - - +
516A HIS* 3.1 31.5 + - + +
1006A GLU* 4.1 9.8 + - - +
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Residues in contact with TRP 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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511A GLN* 3.1 24.1 + - + +
512A THR* 1.3 80.1 - - + +
514A LYS* 1.3 87.0 + - + +
516A HIS* 3.3 14.5 + - + +
517A PHE* 3.1 24.2 + - + -
893A THR* 3.3 27.8 - - - -
896A SER* 3.6 16.6 - - - -
1002A ARG* 6.3 0.2 - - - -
1003A ILE 5.8 0.2 - - - +
1004A ILE* 3.6 37.8 - - + +
1005A ASP 5.5 2.0 - - - +
1006A GLU* 3.5 30.5 + - + +
1016A PHE* 3.5 55.6 - + + -
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Residues in contact with LYS 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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509A PRO* 4.2 12.4 - - + +
510A LYS* 5.3 3.8 - - + +
511A GLN* 3.2 24.9 + - + +
513A TRP* 1.3 124.0 - - + +
515A LYS* 1.3 64.7 + - - +
517A PHE* 3.8 12.2 - - - +
518A LEU* 3.3 24.6 + - - +
891A LEU* 3.2 27.2 + - - -
892A SER 4.1 1.6 + - - -
893A THR* 3.9 16.9 - - - +
896A SER* 4.3 3.6 + - - -
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Residues in contact with LYS 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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509A PRO* 3.9 21.9 - - + +
511A GLN 3.0 12.9 + - - +
512A THR* 3.1 17.5 - - - +
514A LYS* 1.3 79.3 - - - +
516A HIS* 1.3 62.9 + - + +
518A LEU* 4.3 2.2 - - - +
519A ASN* 3.5 23.9 + - - +
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Residues in contact with HIS 516 (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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512A THR* 3.1 37.2 + - + +
513A TRP* 3.5 12.1 - - - +
514A LYS 3.3 0.2 - - - -
515A LYS* 1.3 77.1 - - + +
517A PHE* 1.3 64.1 + - - +
519A ASN* 2.8 27.7 + - - +
520A SER* 3.2 9.9 + - - -
1002A ARG* 5.2 6.7 - - - -
1016A PHE* 4.2 16.6 - + + -
1018A ILE* 4.5 10.3 - - + +
1025A PHE* 4.0 33.5 - + + -
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Residues in contact with PHE 517 (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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494A THR* 5.8 2.0 - - - -
513A TRP* 3.1 15.3 + - + +
514A LYS* 4.0 17.9 - - + +
515A LYS 3.4 0.4 - - - -
516A HIS* 1.3 79.5 - - - +
518A LEU* 1.3 68.2 + - + +
520A SER* 2.8 24.3 + - - -
521A MET* 3.2 39.0 + - + +
890A HIS 3.7 18.8 - - - -
891A LEU* 5.7 1.3 - - - -
892A SER 5.1 0.7 - - - -
895A PHE* 4.2 8.3 - + - -
896A SER* 3.2 46.4 - - - -
1016A PHE* 4.0 17.0 - + + -
1017A VAL* 3.3 28.9 - - + -
1018A ILE* 5.4 0.2 - - - -
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Residues in contact with LEU 518 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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503A GLN* 4.2 26.2 - - + +
505A LYS* 4.9 11.0 - - + -
507A VAL* 4.1 35.2 - - + +
509A PRO* 5.9 5.4 - - + -
514A LYS 3.3 14.8 + - - +
515A LYS* 4.4 2.9 - - - +
517A PHE* 1.3 86.9 - - + +
519A ASN* 1.3 65.3 + - + +
521A MET* 3.0 27.8 + - + +
522A LYS* 3.7 7.2 + - + +
891A LEU* 4.3 17.5 - - + -
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Residues in contact with ASN 519 (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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515A LYS 3.5 14.6 + - - +
516A HIS* 2.8 17.5 + - - +
518A LEU* 1.3 83.6 - - + +
520A SER* 1.3 67.1 + - - +
521A MET 3.2 0.2 - - - -
522A LYS* 3.2 33.0 - - + +
523A ASN* 4.5 2.3 + - - -
591A GLU* 4.8 4.9 - - - +
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Residues in contact with SER 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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516A HIS 3.2 9.1 + - - -
517A PHE* 2.8 18.4 + - - -
518A LEU 3.2 0.2 - - - -
519A ASN* 1.3 82.1 + - - +
521A MET* 1.3 63.8 + - - +
522A LYS 3.1 0.9 - - - -
523A ASN* 3.2 20.8 + - - +
1017A VAL 3.9 8.8 + - - -
1018A ILE* 4.1 11.7 - - - -
1019A THR* 2.8 52.6 + - - -
1020A ARG 5.6 0.4 - - - -
1021A PRO* 6.2 0.2 - - - -
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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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498A SER* 3.5 40.3 - - - +
501A VAL* 4.2 15.6 - - + +
503A GLN* 3.4 31.6 - - + +
517A PHE* 3.2 46.2 + - + +
518A LEU* 3.0 19.0 + - - +
520A SER* 1.3 78.6 + - - +
522A LYS* 1.3 59.8 + - - +
523A ASN 3.0 16.2 + - - +
524A LYS* 5.6 0.2 - - - +
890A HIS* 4.7 11.2 - - - +
895A PHE* 4.1 17.0 - - + -
1019A THR* 4.5 2.0 - - - -
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Residues in contact with LYS 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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503A GLN* 3.2 36.5 + - + +
505A LYS* 5.0 10.4 - - + +
518A LEU* 4.3 4.3 - - + +
519A ASN* 3.2 33.2 - - + +
520A SER 3.1 0.2 - - - -
521A MET* 1.3 77.6 - - - +
523A ASN* 1.3 59.1 + - - +
524A LYS* 3.3 16.5 - - - +
591A GLU* 3.8 35.2 - - + +
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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