Contacts of the helix formed by residues 554 - 561 (chain D) in PDB entry 5COX
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 VAL 554 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315D ILE* 3.8 29.8 - - + -
316D LEU* 5.1 3.4 - - + -
319D GLU* 3.9 34.5 - - + +
551D GLY 5.8 1.1 - - - +
552D GLY* 5.1 2.0 - - - -
553D GLU* 1.3 74.8 - - - +
555D GLY* 1.3 57.5 + - - +
556D PHE 2.6 3.2 + - - -
557D LYS* 2.6 31.8 + - - +
558D ILE* 3.1 14.0 + - + +
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Residues in contact with GLY 555 (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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316D LEU* 4.6 4.9 - - - +
335D ILE* 3.6 31.5 - - - +
550D PHE* 3.9 15.9 + - - +
551D GLY 5.2 0.2 - - - -
552D GLY 4.5 4.2 - - - +
554D VAL* 1.3 82.5 - - - +
556D PHE* 1.3 60.4 + - - +
558D ILE* 3.5 18.9 + - - +
559D ILE* 3.6 11.4 + - - +
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Residues in contact with PHE 556 (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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545D TRP* 3.7 40.6 - + - -
546D LYS* 4.5 9.2 - - - -
547D PRO* 3.8 27.1 - - + -
550D PHE* 3.3 37.1 - + - +
552D GLY 3.5 20.1 + - - +
553D GLU* 3.6 19.1 - - - +
554D VAL 2.6 5.7 + - - -
555D GLY* 1.3 74.2 - - - +
557D LYS* 1.3 62.0 + - - +
559D ILE* 3.3 5.1 + - + +
560D ASN* 2.7 49.4 + - - -
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Residues in contact with LYS 557 (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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553D GLU* 3.0 56.9 + - - +
554D VAL* 2.6 15.4 + - - +
556D PHE* 1.3 82.2 - - + +
558D ILE* 1.3 55.6 + - - +
559D ILE 3.1 1.1 - - - -
560D ASN* 3.4 24.2 - - + +
561D THR* 2.7 47.9 + - + -
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Residues in contact with ILE 558 (chain D).
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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308D GLU* 4.7 2.5 - - - +
311D ARG* 4.8 9.2 - - - +
312D VAL* 3.7 27.1 - - + -
315D ILE* 3.7 34.3 - - + -
316D LEU* 5.5 0.2 - - + -
335D ILE* 3.6 16.6 - - + -
339D GLU* 4.0 19.3 - - - +
554D VAL* 3.1 15.9 + - + +
555D GLY* 3.6 17.5 - - - +
557D LYS* 1.3 77.7 - - - +
559D ILE* 1.3 64.4 + - - +
561D THR* 3.8 5.1 + - - -
562D ALA* 3.3 19.4 + - - +
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Residues in contact with ILE 559 (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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335D ILE* 3.6 28.9 - - + +
338D GLY* 3.3 33.2 - - - +
339D GLU* 4.3 7.4 - - - +
342D LYS* 3.7 8.1 - - - +
361D PHE* 4.2 7.4 - - + -
545D TRP* 3.8 23.3 - - + -
550D PHE* 3.6 51.1 - - + -
555D GLY 3.8 3.4 - - - +
556D PHE 3.3 6.7 + - - +
557D LYS 3.1 0.4 - - - -
558D ILE* 1.3 79.6 - - - +
560D ASN* 1.3 58.8 + - - +
561D THR 2.9 6.8 + - - -
562D ALA* 3.2 14.2 + - - +
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Residues in contact with ASN 560 (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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342D LYS* 3.1 21.6 + - - +
361D PHE* 5.4 5.1 - - - +
545D TRP* 3.6 22.9 - - - -
556D PHE* 2.7 49.2 + - - +
557D LYS* 2.9 30.3 + - + +
559D ILE* 1.3 76.2 - - - +
561D THR* 1.3 61.0 + - + +
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Residues in contact with THR 561 (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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342D LYS* 4.0 2.2 - - - +
557D LYS* 2.7 34.3 + - + +
558D ILE* 3.8 5.0 + - - -
560D ASN* 1.3 79.0 - - + +
562D ALA* 1.3 68.8 + - - +
563D SER* 3.6 8.0 + - - -
566D SER* 4.9 5.2 + - - -
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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