Contacts of the helix formed by residues 550 - 558 (chain D) in PDB entry 5U03
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 550 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328D ILE* 4.6 8.4 - - + +
330D HIS* 5.6 6.5 + - - -
545D LEU* 3.5 26.2 - - + +
548D VAL* 3.5 26.5 - - + +
549D GLY* 1.3 67.9 - - - +
551D LEU* 1.3 51.0 + - - +
552D SER* 3.3 3.4 - - - -
553D HIS* 3.0 44.8 + - - +
554D TYR* 2.7 34.4 + - + +
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Residues in contact with LEU 551 (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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463D VAL* 5.2 8.7 - - + -
467D LEU* 4.4 15.0 - - + -
518D PRO 4.2 11.7 - - - +
519D PHE* 4.0 27.1 - - + -
542D GLY* 4.2 6.3 - - - +
545D LEU* 3.1 45.1 + - + +
546D ALA* 3.9 12.3 - - + +
549D GLY* 5.8 0.2 - - - -
550D ARG* 1.3 70.3 - - - +
552D SER* 1.3 64.1 + - - +
554D TYR* 3.4 4.8 - - - +
555D LEU* 3.0 43.3 + - + +
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Residues in contact with SER 552 (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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549D GLY 5.5 3.0 + - - -
550D ARG 3.3 2.2 - - - +
551D LEU* 1.3 80.4 - - - +
553D HIS* 1.3 62.0 + - - +
555D LEU* 3.4 6.7 + - - +
556D GLN* 2.9 30.4 + - - +
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Residues in contact with HIS 553 (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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550D ARG* 3.0 45.0 + - - +
552D SER* 1.3 82.4 + - - +
554D TYR* 1.4 53.3 + - - +
556D GLN* 3.1 9.3 + - - +
557D LYS* 2.5 71.1 + - + +
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Residues in contact with TYR 554 (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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467D LEU* 4.0 19.0 + - + +
541D PHE* 3.8 28.9 - + - -
545D LEU* 3.6 26.0 - - + -
550D ARG* 2.7 19.3 + - + +
551D LEU* 3.4 12.3 - - + +
553D HIS* 1.4 75.8 - - - +
555D LEU* 1.3 70.7 + - + +
557D LYS* 3.3 9.7 + - + +
558D GLY 3.1 7.3 + - - -
559D CYS* 2.8 68.1 + - - -
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Residues in contact with LEU 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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463D VAL* 4.5 18.4 - - + -
466D LYS* 4.6 24.0 - - + +
467D LEU* 3.9 17.0 - - + -
551D LEU* 3.0 29.8 + - + +
552D SER* 4.0 5.6 - - - +
554D TYR* 1.3 97.9 - - + +
556D GLN* 1.3 63.2 + - - +
558D GLY* 3.1 12.6 + - - -
559D CYS* 3.5 21.7 + - + +
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Residues in contact with GLN 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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552D SER 2.9 19.5 + - - +
553D HIS* 3.4 11.2 - - - +
555D LEU* 1.3 78.9 - - - +
557D LYS* 1.3 61.7 + - - +
558D GLY* 3.3 1.4 + - - -
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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 HIS* 2.5 49.7 + - + +
554D TYR* 3.5 10.1 - - + +
556D GLN* 1.3 73.5 - - - +
558D GLY* 1.3 56.9 + - - +
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Residues in contact with GLY 558 (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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554D TYR 3.1 0.6 + - - -
555D LEU 3.1 9.3 + - - -
556D GLN 4.2 1.3 - - - -
557D LYS* 1.3 81.1 - - - +
559D CYS* 1.4 77.9 + - - +
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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