Contacts of the helix formed by residues 527 - 532 (chain A) in PDB entry 1P1K
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 527 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116A LYS* 3.6 19.0 - - - +
119A ILE* 5.4 3.8 - - + +
125A ASP* 2.9 39.1 + - - -
127A TYR* 5.3 0.2 + - - -
524A ASN* 4.1 1.2 + - - -
525A GLU* 3.5 32.3 + - - +
526A LEU* 1.3 78.0 - - - +
528A PHE* 1.3 60.3 + - - +
529A GLU* 3.1 10.8 - - + +
530A GLU* 3.2 29.3 + - + +
531A ARG* 3.1 32.2 + - - +
32B TYR* 3.6 14.1 + - - -
482B THR* 5.9 0.9 - - - -
498B HIS 5.5 0.6 + - - -
500B VAL* 3.3 39.6 - - - +
505B LYS* 4.5 3.0 - - - +
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Residues in contact with PHE 528 (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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526A LEU* 3.6 16.6 - - + -
527A ARG* 1.3 71.8 - - - +
529A GLU* 1.3 60.6 + - - +
530A GLU 3.0 7.1 + - - -
531A ARG* 3.8 8.3 - - + +
532A LEU* 3.2 52.1 + - + +
30B TYR* 3.6 23.8 - + - -
32B TYR* 3.4 39.4 + + + -
54B TYR* 4.1 18.2 + + - +
56B PHE* 3.9 21.3 - + - -
483B PHE* 3.9 25.4 - + - -
513B PHE* 4.2 8.7 - + - -
516B LEU* 3.7 19.1 - - + -
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Residues in contact with GLU 529 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ILE* 3.8 23.6 - - + +
527A ARG* 3.1 7.0 - - - +
528A PHE* 1.3 80.0 + - - +
530A GLU* 1.3 58.3 + - - +
532A LEU 4.1 6.5 - - - +
32B TYR* 2.6 38.4 + - + -
34B ASN* 2.7 28.9 - - - +
50B THR* 4.7 3.6 + - - -
494B ARG* 4.4 4.3 + - - -
497B PHE* 3.2 28.1 - - + -
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Residues in contact with GLU 530 (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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527A ARG* 3.2 34.5 + - + +
528A PHE 3.0 0.2 - - - -
529A GLU* 1.3 79.3 - - + +
531A ARG* 1.3 65.0 + - + +
532A LEU 3.2 2.0 - - - -
478B TYR* 3.3 8.8 - - - -
482B THR* 3.2 31.7 + - - +
493B THR* 5.8 3.9 - - - +
494B ARG* 3.1 30.7 + - + +
497B PHE* 3.2 50.0 - - + +
498B HIS 4.1 11.6 - - - +
499B PRO* 5.7 3.5 - - - +
500B VAL* 6.0 0.5 - - - +
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Residues in contact with ARG 531 (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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525A GLU 3.0 20.8 + - - -
526A LEU 2.8 31.1 + - - +
527A ARG* 3.1 23.6 + - - +
528A PHE* 4.3 8.1 - - + -
530A GLU* 1.3 79.8 - - + +
532A LEU* 1.3 68.8 + - - +
477B PHE* 3.6 12.8 - - + -
478B TYR* 3.1 23.1 - - - +
480B VAL 4.9 1.3 - - - +
481B LEU* 5.7 0.2 - - - -
482B THR* 3.0 51.2 + - - +
483B PHE* 2.9 69.7 - - - +
509B ALA* 3.8 5.7 - - - +
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Residues in contact with LEU 532 (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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528A PHE* 3.2 41.2 + - + +
529A GLU 4.1 3.8 - - - +
530A GLU 3.2 0.2 - - - -
531A ARG* 1.3 90.9 - - - +
533A LEU* 1.3 66.9 + - - +
54B TYR* 3.3 40.3 + - + +
56B PHE* 4.0 15.9 - - + -
461B TYR* 3.6 30.5 - - + -
463B LYS* 5.5 0.7 - - - -
477B PHE* 3.2 30.5 - - + -
478B TYR* 4.1 0.7 - - - -
494B ARG* 3.1 12.8 + - - -
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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