Contacts of the strand formed by residues 649 - 653 (chain D) in PDB entry 1O23
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 CYS 649 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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582D HIS* 5.4 1.6 - - - -
583D LYS 3.1 7.3 + - - +
584D VAL* 3.4 17.7 - - + -
585D ALA* 3.0 25.1 + - - +
647D TYR* 3.5 1.5 - - - +
648D ASN* 1.3 90.9 - - - +
650D PHE* 1.3 73.0 + - - +
651D VAL* 4.2 1.3 - - - -
667D ARG* 3.6 10.5 - - - -
668D CYS* 2.0 62.1 - - + -
698D LEU 4.0 0.7 - - - -
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Residues in contact with PHE 650 (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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585D ALA* 3.5 18.8 - - + +
587D ILE* 3.9 16.6 - - + -
638D PHE* 3.4 39.9 - + - -
641D ALA* 4.6 1.8 - - + -
642D LEU* 3.2 37.0 - - + -
647D TYR* 4.2 10.5 - - + -
649D CYS* 1.3 87.4 - - - +
651D VAL* 1.3 63.0 + - - +
652D PHE* 3.6 24.3 - + + -
696D SER 3.6 1.0 - - - +
697D ALA* 3.2 3.7 - - - -
698D LEU* 2.9 42.7 + - + +
699D SER 4.9 0.2 - - - -
700D LYS* 3.9 23.8 - - + -
703D PHE* 5.3 1.8 - + + -
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Residues in contact with VAL 651 (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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584D VAL* 3.3 26.7 - - + -
585D ALA 3.0 8.5 + - - +
586D ILE* 3.3 14.3 - - + +
587D ILE* 2.8 26.9 + - - +
649D CYS* 4.6 1.6 - - - -
650D PHE* 1.3 74.1 - - - +
652D PHE* 1.3 63.0 + - - +
653D SER* 3.7 1.0 + - - -
666D TYR* 3.4 50.9 - - + +
667D ARG 4.3 0.2 - - - +
675D ILE* 4.3 2.0 - - + -
695D VAL* 4.0 17.3 - - + -
696D SER 3.3 4.5 - - - +
697D ALA* 4.0 13.5 - - + -
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Residues in contact with PHE 652 (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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587D ILE* 3.4 31.4 - - + -
630D ARG* 4.7 4.4 + - - +
634D LEU* 3.8 49.8 - - + -
638D PHE* 4.9 1.1 - + + -
650D PHE* 3.6 35.4 - + + -
651D VAL* 1.3 73.1 - - - +
653D SER* 1.3 58.5 + - - +
694D GLY 3.5 3.1 - - - +
695D VAL* 3.2 4.4 - - - -
696D SER* 2.8 47.5 + - - +
698D LEU* 4.4 9.2 - - + -
703D PHE* 3.6 29.4 - + - -
709D PHE* 3.7 26.7 - + + -
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Residues in contact with SER 653 (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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586D ILE* 4.4 17.3 - - - -
587D ILE 2.8 10.1 + - - -
588D ILE* 3.2 27.5 - - - +
589D PRO* 3.3 3.0 - - - +
600D TRP* 3.5 19.1 + - - -
651D VAL* 3.7 2.8 + - - -
652D PHE* 1.3 75.5 - - - +
654D ASP* 1.3 78.9 + - - +
657D LEU 4.5 1.4 + - - -
666D TYR* 4.8 2.8 - - - -
694D GLY 3.8 2.9 - - - -
695D VAL* 3.4 25.9 - - - +
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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