Contacts of the helix formed by residues 616 - 624 (chain A) in PDB entry 2IVF
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 SER 616 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A TYR* 3.3 2.5 - - - -
559A LEU* 4.2 7.6 - - - -
614A LYS 3.3 0.8 + - - -
615A ARG* 1.3 72.7 - - - +
617A GLY* 1.3 62.3 + - - +
618A ALA 3.2 3.1 - - - -
619A LYS* 3.1 6.0 + - - +
620A MET* 2.9 20.7 + - - +
898A PHE* 3.3 14.1 - - - -
933A ASP 2.7 17.0 + - - -
934A ILE* 2.7 29.9 + - - +
937A ILE* 2.9 37.5 + - - +
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Residues in contact with GLY 617 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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556A TYR* 3.2 12.1 - - - -
610A PRO 4.2 6.1 - - - -
611A MET* 4.3 1.5 - - - +
614A LYS* 3.0 26.3 + - - -
615A ARG 3.0 2.6 + - - -
616A SER* 1.3 76.8 - - - +
618A ALA* 1.3 58.0 + - - +
620A MET 4.2 0.7 - - - -
621A PHE* 2.7 44.2 + - - +
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Residues in contact with ALA 618 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A MET* 3.5 38.1 + - + +
614A LYS 4.5 0.2 + - - -
616A SER 3.2 1.2 - - - -
617A GLY* 1.3 75.0 - - - +
619A LYS* 1.3 55.7 + - - +
622A PRO* 3.3 19.6 - - - +
929A TRP 4.5 2.5 - - - +
930A LYS* 6.0 0.2 - - + -
931A PRO* 3.4 35.4 - - + -
933A ASP 5.9 0.2 - - - -
934A ILE* 4.2 18.2 - - + +
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Residues in contact with LYS 619 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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616A SER 3.1 8.3 + - - +
618A ALA* 1.3 80.5 - - - +
620A MET* 1.3 66.1 + - - +
621A PHE 3.3 0.7 - - - -
622A PRO* 3.7 1.2 - - - +
623A ASP* 2.4 69.6 + - + +
898A PHE* 4.0 26.7 - - + +
899A ALA* 6.0 1.6 - - + -
934A ILE* 4.0 22.4 - - + +
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Residues in contact with MET 620 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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554A VAL* 3.5 10.2 - - - +
555A GLY* 3.2 37.5 - - - +
556A TYR* 3.6 38.4 - - + +
558A GLN* 4.0 8.5 - - - +
559A LEU* 3.8 19.3 - - + -
616A SER* 2.9 19.2 + - - +
619A LYS* 1.3 81.8 - - - +
621A PHE* 1.3 62.5 + - - +
623A ASP* 5.8 0.7 - - - -
624A VAL* 2.9 42.4 + - + +
625A LEU 3.4 1.7 + - - -
898A PHE* 4.0 22.2 - - - -
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Residues in contact with PHE 621 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A ASP* 3.9 4.0 - - - -
549A TRP* 4.1 7.4 - + - -
550A LEU* 3.9 7.4 - - + -
554A VAL* 3.7 21.3 - - + -
556A TYR* 4.5 2.2 - + - -
603A TYR* 3.4 23.3 - + - -
610A PRO* 3.5 19.3 - - + -
611A MET* 4.5 4.0 - - - -
614A LYS* 3.8 39.0 - - + -
617A GLY* 2.7 26.9 + - - +
620A MET* 1.3 78.3 - - - +
622A PRO* 1.4 63.3 - - + +
625A LEU* 3.1 32.8 + - + -
626A PHE* 2.8 51.1 + + + -
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Residues in contact with PRO 622 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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611A MET* 3.8 19.3 - - + -
617A GLY 3.4 2.2 - - - +
618A ALA 3.3 26.9 - - - +
619A LYS 3.7 2.9 - - - +
621A PHE* 1.4 93.9 - - + +
623A ASP* 1.3 63.1 + - - +
626A PHE* 3.6 19.9 - - + +
627A PRO* 3.1 25.6 - - - +
645A TYR* 4.5 12.6 - - + +
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Residues in contact with ASP 623 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619A LYS* 2.4 62.8 + - + +
620A MET* 4.8 0.9 - - - -
622A PRO* 1.3 84.7 - - - +
624A VAL* 1.3 69.6 + - + +
627A PRO* 3.9 10.3 - - - +
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Residues in contact with VAL 624 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553A HIS 3.8 9.2 - - - +
554A VAL 3.5 31.9 - - - +
555A GLY* 3.7 8.1 - - - +
558A GLN* 4.9 4.3 - - - +
620A MET* 2.9 32.7 + - + +
623A ASP* 1.3 89.8 - - + +
625A LEU* 1.3 64.7 + - - +
626A PHE 3.8 0.2 - - - -
627A PRO* 3.8 7.9 - - - +
628A LYS* 3.6 22.8 - - - +
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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