Contacts of the strand formed by residues 846 - 853 (chain C) in PDB entry 2A69
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 846 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557C ARG* 4.4 4.9 + - - +
560C MET* 4.8 10.5 - - + -
564C MET* 3.7 34.1 - - + -
686C ASP* 3.9 16.6 - - - +
688C ILE* 4.7 1.6 - - - +
838C LYS* 3.1 34.2 - - + +
839C LEU 4.1 0.7 - - - +
840C ALA* 3.5 8.1 - - + -
844C GLY 2.6 10.5 + - - +
845C ASN* 1.3 84.3 + - - +
847C GLY* 1.3 60.7 + - - +
879C ARG* 4.7 1.0 + - - -
997C LEU* 3.8 2.5 - - + +
9138C MG 3.2 21.3 - - - -
741D ASP* 2.9 48.2 + - + +
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Residues in contact with GLY 847 (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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686C ASP 3.5 8.5 - - - -
688C ILE* 3.3 20.7 - - - +
838C LYS* 3.3 4.2 - - - -
839C LEU* 3.0 34.0 + - - +
846C LYS* 1.3 83.2 - - - +
848C VAL* 1.3 63.8 + - - -
740D PHE 3.5 7.0 - - - -
741D ASP* 4.4 1.1 - - - -
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Residues in contact with VAL 848 (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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686C ASP 3.4 2.4 + - - -
687C ALA* 3.5 4.7 - - - +
688C ILE* 2.7 34.5 + - - -
835C VAL 3.5 7.4 - - - +
836C GLY 3.7 9.0 - - - +
837C ASP 3.3 14.1 - - - +
838C LYS* 4.0 13.9 - - + -
847C GLY* 1.3 77.0 - - - -
849C VAL* 1.3 59.7 + - - +
850C ALA* 3.4 0.7 + - - +
630D VAL* 4.7 6.5 - - + -
631D ILE 4.5 0.9 - - - +
632D VAL* 3.4 32.1 - - + -
740D PHE* 3.3 23.1 + - + +
741D ASP 4.5 0.2 - - - -
742D GLY* 4.0 18.6 - - - +
9028D MG 4.2 4.9 - - - -
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Residues in contact with VAL 849 (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 ILE* 3.4 11.7 - - + +
690C ILE* 3.5 33.9 - - + -
833C LEU* 3.8 17.0 - - + -
834C GLN 4.2 0.9 - - - +
835C VAL* 2.5 47.2 - - - +
837C ASP 3.0 9.6 + - - +
839C LEU* 3.3 35.9 - - + -
848C VAL* 1.3 75.2 - - - +
850C ALA* 1.3 63.1 + - - +
851C LYS 4.0 6.3 - - - +
852C ILE* 4.2 4.3 - - + -
632D VAL* 3.9 1.6 - - - +
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Residues in contact with ALA 850 (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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682C TYR* 3.2 36.0 - - + +
687C ALA* 4.0 4.3 - - + -
688C ILE 2.8 7.1 + - - -
835C VAL* 4.5 9.2 - - - +
848C VAL 3.4 0.8 + - - +
849C VAL* 1.3 75.1 - - - +
851C LYS* 1.3 64.1 + - - +
632D VAL* 3.4 19.9 - - + +
633D VAL* 3.4 25.3 - - + +
727D GLN* 5.2 5.5 - - - +
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Residues in contact with LYS 851 (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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682C TYR* 3.3 49.7 + - + -
688C ILE 3.9 1.8 + - - -
689C VAL* 3.7 4.5 - - + +
690C ILE* 3.1 26.8 + - - +
849C VAL* 3.6 1.8 - - - +
850C ALA* 1.3 84.4 - - - +
852C ILE* 1.3 89.4 + - + +
853C LEU* 3.5 28.4 + - + +
854C PRO* 5.5 3.6 - - - -
636D GLN* 5.2 2.6 - - - +
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Residues in contact with ILE 852 (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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30B ARG* 4.6 8.7 + - - -
690C ILE* 3.1 28.0 - - + +
691C SER 4.3 0.7 - - - +
692C GLU* 3.8 25.0 - - + +
695C LEU* 4.6 19.3 - - + -
833C LEU* 6.6 0.2 - - + -
834C GLN* 5.2 5.2 - - - -
835C VAL* 3.9 36.3 - - + +
849C VAL* 4.2 5.8 - - + -
851C LYS* 1.3 93.1 - - + +
853C LEU* 1.3 61.5 + - - +
854C PRO* 4.0 1.7 - - - +
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Residues in contact with LEU 853 (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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679C PHE* 3.6 32.1 - - + -
682C TYR* 5.4 4.7 - - + -
689C VAL* 3.9 13.0 - - + -
690C ILE 2.7 8.5 + - - +
691C SER* 3.6 1.0 - - - -
692C GLU* 2.6 34.1 + - - +
851C LYS* 3.5 31.8 + - + +
852C ILE* 1.3 74.0 - - - +
854C PRO* 1.4 69.8 - - + +
857C ASP* 4.4 5.2 - - - +
858C MET* 3.4 51.6 - - + +
870C ILE* 4.7 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