Contacts of the strand formed by residues 611 - 615 (chain D) in PDB entry 5DFV
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 611 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398C ARG 6.0 0.2 - - - -
401C TRP* 4.9 2.5 - - - +
602D TYR* 3.2 7.5 - - - -
603D GLN* 2.6 61.2 + - + +
608D GLN* 6.1 4.0 - - - +
609D PRO 4.7 2.2 - - - +
610D PRO* 1.3 76.1 - - - +
612D LEU* 1.3 68.5 + - - +
613D LEU* 3.5 19.3 + - + +
701D GLY 5.4 4.8 + - - -
702D VAL* 4.7 12.4 - - - +
703D PRO* 5.9 3.8 - - - +
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Residues in contact with LEU 612 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C LEU* 4.0 32.3 - - + -
397C LEU 3.8 12.6 + - - +
398C ARG* 4.3 12.0 + - - +
401C TRP* 5.1 0.6 - - - +
599D HIS* 4.1 9.4 - - + -
601D TRP 3.9 7.6 - - - +
602D TYR* 3.3 44.0 - - + +
611D LYS* 1.3 76.9 - - - +
613D LEU* 1.3 64.5 + - - +
614D ILE 4.0 13.2 - - - +
615D LYS* 4.3 4.3 - - + -
698D GLU* 3.6 45.1 - - + +
702D VAL* 4.3 3.6 - - - +
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Residues in contact with LEU 613 (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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601D TRP* 3.0 15.6 + - + +
602D TYR 4.8 0.9 - - - -
603D GLN* 3.5 38.4 - - + +
611D LYS* 3.8 31.0 - - - +
612D LEU* 1.3 82.1 - - - +
614D ILE* 1.3 67.9 + - + +
697D LEU* 3.6 3.3 - - - -
698D GLU* 2.7 33.8 + - - +
702D VAL* 4.2 22.3 - - + +
706D PHE* 3.9 23.3 - - + -
719D LEU* 5.3 2.9 - - + -
732D TYR* 3.7 21.1 - - + -
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Residues in contact with ILE 614 (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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599D HIS* 3.5 3.6 - - - +
601D TRP* 2.9 49.7 + - + +
612D LEU* 4.0 2.6 - - - +
613D LEU* 1.3 88.3 - - + +
615D LYS* 1.3 62.2 + - - +
694D ALA* 3.1 37.9 - - - +
695D SER* 3.8 5.4 - - - +
696D TYR 3.5 9.4 - - - +
697D LEU* 4.0 22.2 - - + -
706D PHE* 4.0 17.9 - - + -
707D SER* 4.1 4.0 - - - +
708D GLY* 4.1 17.0 - - - +
719D LEU* 4.0 15.7 - - + -
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Residues in contact with LYS 615 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396C LEU* 3.6 33.4 - - + -
398C ARG* 4.1 14.6 - - - +
599D HIS* 3.9 4.9 - - - +
612D LEU* 4.3 8.1 - - + -
614D ILE* 1.3 73.2 - - - +
651D TYR* 1.3 83.9 + - + +
694D ALA 3.4 2.0 - - - -
696D TYR* 2.8 46.6 + - + +
697D LEU 3.7 19.4 + - - -
698D GLU* 3.8 26.1 - - + +
699D SER 4.7 2.4 - - - +
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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