Contacts of the helix formed by residues 620 - 625 (chain C) in PDB entry 2XER
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 LEU 620 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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616C THR* 3.0 26.0 + - + +
617C ALA* 3.1 17.4 + - - +
619C ASN* 1.3 74.0 - - - +
621C PRO* 1.3 75.4 - - + +
622C PHE 3.1 1.3 - - - -
623C LEU* 3.0 5.3 + - + -
624C ILE* 2.9 42.9 + - + +
633C LEU* 4.7 6.7 - - + -
659C LEU* 3.7 24.0 - - + -
679C VAL* 4.1 11.0 - - + -
684C PHE* 4.2 16.4 - - + -
685C GLY* 4.4 17.3 - - - +
688C LEU* 4.5 16.4 - - + -
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Residues in contact with PRO 621 (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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617C ALA 4.3 1.6 - - - +
618C ARG 4.3 8.1 - - - +
619C ASN* 3.8 1.3 - - - -
620C LEU* 1.3 97.0 - - + +
622C PHE* 1.3 61.0 + - - +
624C ILE* 3.4 10.5 + - + +
625C LYS* 3.4 18.9 + - - +
659C LEU* 5.6 4.7 - - + +
675C HIS* 4.3 24.9 - - + +
678C ALA* 3.8 27.8 - - + +
679C VAL* 4.4 15.3 - - + -
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Residues in contact with PHE 622 (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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585C VAL* 3.8 24.5 - - + -
589C CYS* 3.7 23.1 - - - -
619C ASN* 3.7 15.2 + - + +
620C LEU 3.1 0.6 - - - -
621C PRO* 1.3 78.8 - - - +
623C LEU* 1.3 66.9 + - + +
624C ILE 3.3 0.3 + - - -
625C LYS* 3.4 9.1 + - + +
626C LYS* 3.4 47.8 + - - +
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Residues in contact with LEU 623 (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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584C PHE* 5.2 1.3 - - + -
585C VAL* 3.8 19.7 - - + +
588C MET* 3.3 60.1 - - + +
589C CYS* 4.0 9.2 - - - -
615C THR 5.3 0.4 - - - +
616C THR* 4.1 32.8 - - + +
619C ASN* 3.1 24.2 + - + +
620C LEU* 3.0 6.8 + - + +
622C PHE* 1.3 77.0 - - + +
624C ILE* 1.3 59.9 - - - +
626C LYS* 3.3 7.4 + - - +
627C ASP* 3.1 21.8 + - - +
633C LEU* 3.9 13.9 - - + +
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Residues in contact with ILE 624 (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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620C LEU* 2.9 39.7 + - + +
621C PRO* 3.5 13.5 - - + +
622C PHE 3.2 0.2 - - - -
623C LEU* 1.3 74.7 - - - +
625C LYS* 1.3 62.7 + - - +
627C ASP* 2.9 19.5 + - + +
628C ALA* 3.3 9.9 + - - +
633C LEU* 4.1 9.0 - - + -
678C ALA* 3.9 16.6 - - + +
679C VAL* 4.1 9.4 - - - -
682C ASN* 3.1 50.9 - - + +
685C GLY* 4.7 2.7 - - - -
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Residues in contact with LYS 625 (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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621C PRO 3.4 9.0 + - - +
622C PHE* 3.8 12.3 - - + +
623C LEU 3.4 0.2 - - - -
624C ILE* 1.3 79.6 - - - +
626C LYS* 1.3 67.6 + - + +
627C ASP 3.2 1.4 + - - -
628C ALA* 3.3 28.4 + - + +
629C GLN* 4.6 6.5 + - - +
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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