Contacts of the helix formed by residues 528 - 536 (chain D) in PDB entry 5MKF
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 528 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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523D GLY 3.6 0.2 + - - -
524D ILE* 3.0 42.2 + - + +
527D TYR* 1.3 111.8 - - + +
529D THR* 1.3 64.8 + - + +
530D SER 3.6 0.5 + - - -
531D ASN* 4.3 2.1 + - - +
532D VAL* 3.4 20.8 + - - +
554D TRP* 3.7 44.3 - - + +
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Residues in contact with THR 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D ARG* 5.8 0.5 + - - -
524D ILE 3.1 11.0 + - - +
525D ASN* 2.1 35.3 + - - +
528D ARG* 1.3 81.6 - - + +
530D SER* 1.3 65.5 + - - +
531D ASN 3.6 0.2 - - - -
532D VAL* 3.2 24.3 - - + +
533D GLU* 3.2 20.2 + - - +
551D LEU 4.3 13.9 - - - +
554D TRP* 4.1 24.9 - - + -
555D GLN* 5.6 0.9 - - - +
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Residues in contact with SER 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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464D ARG* 5.9 4.0 - - - +
525D ASN 3.1 2.9 + - - -
526D ILE* 2.2 60.5 + - - +
527D TYR* 4.4 0.7 + - - -
529D THR* 1.3 68.7 - - - +
531D ASN* 1.3 72.7 + - - +
533D GLU* 2.9 28.3 + - - +
534D VAL* 3.3 14.0 + - - +
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Residues in contact with ASN 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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526D ILE 4.0 1.0 + - - -
527D TYR 5.0 4.7 - - - +
528D ARG 4.3 5.0 + - - +
530D SER* 1.3 82.8 + - - +
532D VAL* 1.3 62.5 + - - +
534D VAL* 3.3 17.4 + - - +
535D LEU* 3.0 33.8 + - + +
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Residues in contact with VAL 532 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462D LEU* 5.5 1.3 - - + -
528D ARG 3.4 20.2 + - - +
529D THR* 3.2 17.7 - - + +
531D ASN* 1.3 77.6 - - - +
533D GLU* 1.3 69.7 + - + +
535D LEU* 2.9 32.7 + - + +
536D LEU* 3.2 8.2 + - + +
548D PHE* 5.2 5.6 - - + -
551D LEU* 3.5 58.3 - - + +
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Residues in contact with GLU 533 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461D LYS 4.8 1.4 - - - +
462D LEU* 2.7 56.7 - - + +
463D ILE* 4.6 6.1 - - + +
464D ARG* 3.1 37.3 + - - +
529D THR* 3.3 19.2 + - - +
530D SER* 2.9 18.7 + - - +
532D VAL* 1.3 76.9 - - + +
534D VAL* 1.3 59.0 + - + +
536D LEU* 2.8 26.5 + - - +
540D GLU* 5.2 0.2 - - - +
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Residues in contact with VAL 534 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530D SER 3.3 12.1 + - - +
531D ASN* 3.5 20.4 - - - +
532D VAL 3.1 0.6 - - - -
533D GLU* 1.3 80.0 - - + +
535D LEU* 1.3 60.4 + - - +
536D LEU 2.8 15.9 + - - +
537D GLN* 3.7 8.0 + - - +
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Residues in contact with LEU 535 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531D ASN* 3.0 32.5 + - - +
532D VAL* 2.9 23.7 + - + +
534D VAL* 1.3 76.6 - - + +
536D LEU* 1.3 77.5 + - + +
537D GLN 3.8 1.1 + - - -
539D LEU* 3.2 34.5 - - + +
551D LEU* 4.9 5.2 - - + -
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Residues in contact with LEU 536 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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436D PHE* 5.7 2.2 - - + -
462D LEU* 4.8 2.6 - - + +
532D VAL* 3.2 10.2 + - + +
533D GLU* 2.8 24.6 - - - +
534D VAL 2.8 5.2 + - - +
535D LEU* 1.3 96.6 - - + +
537D GLN* 1.3 56.3 + - - +
539D LEU* 3.6 18.4 - - + -
540D GLU* 2.7 52.3 - - + +
546D PRO* 4.7 8.1 - - + -
548D PHE* 3.7 35.7 - - + -
551D LEU* 3.6 20.2 - - + -
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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