Contacts of the helix formed by residues 688 - 698 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634C TYR* 4.1 5.8 - - + -
637C SER* 4.1 24.2 - - - +
638C MET* 3.7 22.0 - - - -
656C VAL 3.8 8.7 - - - +
657C SER* 3.1 25.7 + - - +
687C THR* 1.3 71.4 - - - +
689C MET* 1.3 70.2 + - - +
690C SER 3.2 0.4 - - - -
691C ARG* 3.0 16.8 + - - +
692C ALA* 3.5 6.8 + - - -
695C PHE* 4.3 9.8 - - + -
719C ILE* 3.4 42.0 - - + -
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Residues in contact with MET 689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657C SER* 3.5 32.3 - - - +
658C ARG* 3.6 28.7 - - + -
661C TYR* 4.4 0.4 - - + -
687C THR* 3.4 2.0 - - - -
688C VAL* 1.3 80.3 - - - +
690C SER* 1.3 60.5 + - - +
691C ARG 3.1 1.4 + - - -
692C ALA* 3.1 19.6 + - - +
718C GLN* 3.1 33.7 - - + +
719C ILE* 3.8 15.7 - - - +
722C ALA* 3.6 17.8 - - + +
244D GLU* 3.3 45.1 - - + +
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Residues in contact with SER 690 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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684C ARG 4.5 4.9 + - - -
685C ASN* 4.1 10.6 + - - -
687C THR* 2.9 33.5 + - - -
689C MET* 1.3 77.5 - - - +
691C ARG* 1.3 62.1 + - - +
692C ALA 3.5 0.9 - - - -
693C GLU* 5.1 2.6 + - - +
244D GLU* 5.1 0.4 + - - -
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Residues in contact with ARG 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599C GLY 4.2 9.5 + - - -
600C THR* 5.9 0.2 - - - +
603C VAL* 4.5 6.5 - - - +
637C SER 5.6 0.2 - - - +
638C MET* 2.9 62.0 + - - +
641C GLY* 3.4 26.9 - - - +
642C SER* 4.0 14.5 - - - +
685C ASN* 5.0 8.9 + - - -
686C SER* 5.8 0.2 - - - +
687C THR 3.9 9.1 + - - +
688C VAL* 3.0 10.3 + - - +
690C SER* 1.3 82.8 - - - +
692C ALA* 1.3 64.5 + - - +
693C GLU* 3.1 5.1 + - - -
694C ASN* 3.1 20.2 + - - +
695C PHE* 3.2 12.2 - - + -
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Residues in contact with ALA 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688C VAL 3.5 2.7 + - - +
689C MET 3.1 17.2 + - - +
690C SER 3.5 0.8 - - - -
691C ARG* 1.3 77.1 - - - +
693C GLU* 1.3 63.8 + - - +
695C PHE* 3.1 30.4 + - - +
722C ALA* 3.8 16.4 - - + +
723C LEU* 3.5 17.9 - - + -
726C VAL* 3.7 18.8 - - + -
728C VAL* 3.5 9.5 - - - +
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Residues in contact with GLU 693 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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690C SER 5.1 2.4 + - - +
691C ARG* 3.1 2.3 + - - -
692C ALA* 1.3 78.6 - - - +
694C ASN* 1.3 65.0 + - - +
695C PHE 3.1 4.3 + - - -
696C LYS* 3.2 55.2 + - + +
726C VAL* 3.8 24.2 - - + +
728C VAL* 4.8 0.2 - - - -
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Residues in contact with ASN 694 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346B ILE* 5.4 6.4 - - - +
392B LYS* 5.8 3.2 - - - +
640C LEU 3.6 10.4 - - - +
641C GLY 3.2 31.7 + - - +
642C SER 4.4 3.6 + - - -
643C GLY* 4.1 15.4 + - - +
691C ARG* 3.1 11.3 + - - +
693C GLU* 1.3 81.1 - - - +
695C PHE* 1.3 57.9 + - - +
696C LYS* 3.2 5.8 - - - -
697C GLN* 3.4 31.7 + - - +
698C VAL* 4.5 0.5 - - - +
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Residues in contact with PHE 695 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637C SER* 3.2 29.8 - - - -
640C LEU* 3.8 15.3 - - + -
641C GLY* 3.7 12.3 - - - -
688C VAL* 4.3 14.4 - - + -
691C ARG* 3.2 32.5 - - + -
692C ALA* 3.1 20.7 + - - +
694C ASN* 1.3 75.2 - - - +
696C LYS* 1.3 61.6 + - - +
697C GLN 3.2 2.9 - - - -
698C VAL* 3.2 31.9 + - + +
700C TYR* 3.8 49.7 - + + +
719C ILE* 5.6 0.9 - - + -
723C LEU* 3.8 9.9 - - + -
728C VAL* 3.5 23.1 - - + +
729C ASP 4.9 0.7 - - - +
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Residues in contact with LYS 696 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B ILE* 6.0 4.4 - - - +
317B ARG* 5.9 2.6 - - - +
693C GLU* 3.2 42.3 + - + +
694C ASN 3.2 1.8 - - - -
695C PHE* 1.3 78.1 - - - +
697C GLN* 1.3 59.2 + - + +
698C VAL 3.4 2.8 + - - +
726C VAL 3.7 19.6 + - - -
727C GLY 4.9 3.6 - - - +
728C VAL* 3.5 18.8 - - + -
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Residues in contact with GLN 697 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341B VAL* 4.0 25.9 - - + +
344B GLN* 5.2 3.5 - - - +
346B ILE* 5.3 10.5 - - - +
640C LEU 5.5 0.2 - - - +
643C GLY* 3.5 30.9 + - - +
645C GLY* 4.3 12.0 + - - -
647C PHE 4.5 3.6 - - - +
648C LYS* 4.6 2.3 - - - +
694C ASN* 3.4 29.9 + - - +
696C LYS* 1.3 77.4 - - + +
698C VAL* 1.3 67.7 + - + +
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Residues in contact with VAL 698 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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640C LEU* 3.8 47.8 - - + +
645C GLY* 6.2 2.5 - - - -
647C PHE* 3.4 22.2 - - + +
648C LYS 3.6 6.5 - - - +
694C ASN 4.5 0.2 - - - +
695C PHE* 3.2 42.7 - - + +
696C LYS 3.4 2.7 + - - +
697C GLN* 1.3 91.5 - - + +
699C GLU* 1.3 65.7 + - - +
700C TYR* 3.8 2.8 + - + +
729C ASP 5.0 5.4 - - - +
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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