Contacts of the strand formed by residues 455 - 460 (chain D) in PDB entry 4QG0
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 LYS 455 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D LEU* 3.5 16.5 + - + +
454D PHE* 1.3 71.3 - - - +
456D TYR* 1.3 63.6 + - - +
457D VAL* 3.4 1.2 + - - +
553D TYR* 3.1 6.5 - - - -
554D CYS* 2.8 41.5 + - + +
556D LYS 4.5 1.3 - - - +
557D VAL* 3.8 37.9 - - + +
559D ARG* 6.2 1.6 - - - +
562D LEU* 4.0 35.7 - - + -
702D DGT 3.1 42.5 + - - -
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Residues in contact with TYR 456 (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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377D LYS* 3.6 47.8 - - + -
378D VAL* 5.7 2.2 - - + -
454D PHE 3.8 3.2 + - - -
455D LYS* 1.3 75.3 - - - +
457D VAL* 1.3 61.9 + - - +
458D GLY* 3.6 26.4 - - - -
459D GLU* 3.2 29.5 + - - +
551D ARG* 4.1 15.7 - - + -
552D VAL 4.0 2.7 - - - -
553D TYR* 3.7 28.7 - + + -
562D LEU* 4.1 12.6 - - - +
566D ARG* 5.0 4.9 + - - -
583D ASP* 6.0 2.7 - - - -
702D DGT 5.1 11.0 + - - +
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Residues in contact with VAL 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455D LYS 3.6 2.2 - - - +
456D TYR* 1.3 78.8 - - - +
458D GLY* 1.3 58.6 + - - +
498D PHE* 5.4 0.2 - - + -
552D VAL* 2.7 28.3 + - + +
553D TYR 3.5 23.6 - - - -
554D CYS* 3.6 15.5 - - + +
562D LEU* 4.5 6.1 - - + -
565D ALA* 3.6 35.2 - - + +
566D ARG* 3.7 17.1 + - + +
569D PHE* 3.7 17.4 - - + -
583D ASP* 5.2 2.9 - - - +
587D ILE* 4.1 17.7 - - - +
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Residues in contact with GLY 458 (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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456D TYR* 3.4 18.3 - - - -
457D VAL* 1.3 85.0 - - - +
459D GLU* 1.3 60.4 + - - -
550D ILE 3.7 0.7 - - - +
551D ARG* 3.3 4.0 - - - -
552D VAL 2.9 27.7 + - - -
569D PHE* 3.5 18.7 - - - -
581D PRO* 5.8 0.2 - - - -
583D ASP* 5.7 3.6 - - - -
587D ILE* 5.8 0.2 - - - -
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Residues in contact with GLU 459 (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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456D TYR* 3.2 18.1 + - - +
458D GLY* 1.3 72.6 - - - +
460D THR* 1.3 72.4 + - - +
461D GLN* 5.7 0.9 - - + -
549D LEU* 3.5 22.3 - - + +
550D ILE 3.2 11.2 - - - +
551D ARG* 2.4 43.3 + - + +
569D PHE* 3.6 3.6 - - - -
581D PRO* 3.8 23.7 - - - +
582D GLN* 4.9 8.7 + - - +
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Residues in contact with THR 460 (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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459D GLU* 1.3 78.5 - - - +
461D GLN* 1.3 71.5 + - - +
549D LEU* 4.0 0.5 - - - -
550D ILE* 2.9 46.5 + - + +
569D PHE* 4.1 6.5 - - + -
572D TRP* 4.4 2.9 - - + -
573D CYS* 3.6 27.9 - - - -
578D PHE* 3.3 28.9 - - + +
579D THR* 2.6 30.5 + - - -
581D PRO* 4.8 0.2 - - - -
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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