Contacts of the helix formed by residues 688 - 698 (chain D) in PDB entry 5Y7K
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 688 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634D TYR* 3.8 5.8 - - + -
637D SER* 4.1 24.2 - - - +
638D MET* 3.6 22.4 - - - +
656D VAL 3.6 16.2 - - - +
657D SER* 3.0 16.5 + - - +
687D THR* 1.3 72.3 - - - +
689D MET* 1.3 76.0 + - - +
690D SER 3.2 0.7 - - - -
691D ARG* 3.0 20.0 + - - +
692D ALA* 3.7 4.2 + - - +
695D PHE* 4.4 8.2 - - + -
719D ILE* 3.3 42.8 - - + -
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Residues in contact with MET 689 (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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244C GLU* 3.2 50.9 - - + +
657D SER* 3.4 45.5 - - - +
658D ARG* 4.0 6.7 - - + -
661D TYR* 4.7 0.2 - - + -
687D THR* 3.3 6.7 - - - +
688D VAL* 1.3 87.6 - - - +
690D SER* 1.3 56.5 + - - +
691D ARG 2.9 6.4 + - - -
692D ALA* 2.9 20.9 + - - +
718D GLN* 3.5 14.8 - - + +
719D ILE* 3.9 13.9 - - - +
722D ALA* 3.4 30.1 - - + +
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Residues in contact with SER 690 (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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684D ARG 4.4 6.7 + - - -
685D ASN* 4.3 8.4 + - - -
687D THR* 3.0 32.9 + - - -
689D MET* 1.3 75.7 - - - +
691D ARG* 1.3 63.2 + - - +
692D ALA 3.6 0.2 - - - -
693D GLU* 6.1 0.3 - - - +
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Residues in contact with ARG 691 (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 GLY 4.1 10.3 + - - -
603D VAL* 4.5 5.7 - - - +
637D SER 5.6 0.2 - - - +
638D MET* 2.8 65.2 + - - +
641D GLY* 3.2 29.4 - - - +
642D SER* 3.9 16.0 - - - -
685D ASN 4.9 7.5 + - - -
687D THR 4.1 5.1 + - - +
688D VAL* 3.0 9.1 + - - +
689D MET 2.9 1.8 + - - -
690D SER* 1.3 88.1 + - - +
692D ALA* 1.3 66.1 + - - +
693D GLU* 3.1 4.0 - - - -
694D ASN* 3.0 21.7 + - - +
695D PHE* 3.2 13.4 - - + -
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Residues in contact with ALA 692 (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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688D VAL 3.7 2.1 + - - -
689D MET* 2.9 16.9 + - - +
690D SER 3.6 0.8 - - - -
691D ARG* 1.3 77.6 - - - +
693D GLU* 1.3 64.4 + - - +
695D PHE* 3.1 19.8 + - - +
722D ALA* 3.6 31.0 - - + +
723D LEU* 3.7 24.8 - - + +
726D VAL* 3.8 9.6 - - + -
728D VAL* 3.8 7.6 - - - +
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Residues in contact with GLU 693 (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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690D SER 6.1 0.2 - - - +
691D ARG 3.1 1.9 + - - -
692D ALA* 1.3 78.6 - - - +
694D ASN* 1.3 68.5 + - - +
695D PHE 3.1 1.7 + - - -
696D LYS* 3.0 58.1 + - - +
697D GLN* 5.2 0.3 + - - -
726D VAL* 3.7 23.7 - - + +
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Residues in contact with ASN 694 (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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640D LEU 4.0 7.4 - - - +
641D GLY* 2.8 38.6 + - - +
642D SER 4.3 4.2 + - - -
643D GLY* 4.1 14.0 + - - +
690D SER 5.6 0.2 + - - -
691D ARG* 3.0 14.8 + - - +
693D GLU* 1.3 80.6 - - - +
695D PHE* 1.3 61.7 + - - +
696D LYS 3.0 2.7 + - - -
697D GLN* 3.2 38.8 + - - +
698D VAL 4.6 0.5 + - - -
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Residues in contact with PHE 695 (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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637D SER* 3.2 31.4 - - - -
640D LEU* 3.9 9.9 - - + -
641D GLY* 3.8 13.7 - - - -
688D VAL* 4.4 12.6 - - + -
691D ARG* 3.2 30.5 - - + -
692D ALA* 3.1 16.0 + - - +
693D GLU 3.1 1.8 + - - -
694D ASN* 1.3 72.2 - - - +
696D LYS* 1.3 59.7 + - - +
697D GLN 3.0 6.0 + - - -
698D VAL* 3.2 31.9 + - + +
700D TYR* 3.4 56.1 - + + +
719D ILE* 5.7 3.4 - - + -
723D LEU* 3.8 18.2 - - + -
728D VAL* 3.4 14.4 - - + +
729D ASP 5.0 0.3 - - - +
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Residues in contact with LYS 696 (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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693D GLU* 3.0 45.8 - - - +
694D ASN 3.0 1.2 - - - -
695D PHE* 1.3 78.2 - - - +
697D GLN* 1.3 61.2 + - + +
698D VAL 3.5 2.2 - - - +
726D VAL* 2.8 29.3 + - - -
727D GLY* 3.0 19.6 + - - -
728D VAL* 3.8 17.7 - - + -
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Residues in contact with GLN 697 (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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643D GLY* 4.0 23.2 - - - +
645D GLY* 4.9 8.2 + - - -
647D PHE 4.7 2.4 - - - +
648D LYS* 4.7 2.3 - - - +
693D GLU 5.2 0.8 + - - +
694D ASN* 3.2 38.9 + - - +
695D PHE 3.0 1.4 - - - -
696D LYS* 1.3 84.0 - - + +
698D VAL* 1.3 65.1 + - + +
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Residues in contact with VAL 698 (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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640D LEU* 3.8 55.2 - - + +
645D GLY* 6.4 1.6 - - - -
647D PHE* 3.6 19.7 - - + +
648D LYS 3.5 9.0 - - - +
695D PHE* 3.2 33.8 - - + +
696D LYS 3.5 2.1 - - - +
697D GLN* 1.3 90.7 - - + +
699D GLU* 1.3 69.0 + - - +
700D TYR* 3.9 2.3 + - + +
729D ASP 5.1 4.5 - - - +
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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