Contacts of the helix formed by residues 700 - 711 (chain B) in PDB entry 2IVS
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 GLY 700 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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924A PHE* 2.8 34.8 + - - +
925A ASP* 4.9 1.6 + - - -
926A HIS* 4.9 0.9 - - - -
701B PRO* 1.3 78.8 - - - +
703B SER* 2.9 28.4 + - - -
704B LEU* 3.1 18.6 + - - +
3013B FMT 3.1 7.9 + - - -
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Residues in contact with PRO 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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908A ARG 5.2 6.5 - - - +
910A GLN* 4.0 9.6 - - - +
926A HIS* 4.0 11.9 - - + +
700B GLY* 1.3 80.9 - - - +
702B LEU* 1.3 59.6 + - - +
704B LEU* 3.5 13.3 + - + +
705B SER* 3.1 26.6 + - - -
3013B FMT 3.2 10.5 - - - +
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Residues in contact with LEU 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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910A GLN* 3.4 15.3 - - - +
961A PHE* 3.9 20.2 - - + -
701B PRO* 1.3 76.2 - - - +
703B SER* 1.3 66.6 + - - +
705B SER* 3.0 5.5 + - - -
706B VAL* 2.8 33.1 + - + +
766B PRO* 3.3 41.1 - - + +
769B LEU* 4.0 8.5 - - + -
770B ARG* 3.8 28.7 - - + +
773B LEU* 3.9 19.7 - - + -
3013B FMT 2.9 17.4 + - - +
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Residues in contact with SER 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
924A PHE* 3.7 20.6 - - - -
961A PHE* 3.6 31.1 - - - +
700B GLY 2.9 27.4 + - - -
702B LEU* 1.3 75.5 - - - +
704B LEU* 1.3 58.9 + - - +
706B VAL* 3.9 3.8 - - - +
707B ASP* 3.0 31.7 + - - +
3013B FMT 2.9 13.7 + - - -
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Residues in contact with LEU 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700B GLY 3.1 16.7 + - - +
701B PRO* 3.6 13.2 - - + +
702B LEU 3.1 0.6 - - - -
703B SER* 1.3 85.4 + - - +
705B SER* 1.3 57.8 + - - +
707B ASP* 3.9 3.3 - - - +
708B ALA* 3.0 28.9 + - - +
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Residues in contact with SER 705 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701B PRO 3.1 12.2 + - - -
702B LEU* 3.0 12.1 + - - -
704B LEU* 1.3 74.5 - - - +
706B VAL* 1.3 60.5 + - - +
708B ALA* 3.5 6.3 + - - +
709B PHE* 3.0 28.9 + - - +
773B LEU* 3.8 22.0 - - - +
777B ASN* 5.9 3.4 - - - -
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Residues in contact with VAL 706 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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958A GLU* 4.0 23.3 - - + +
961A PHE* 4.1 13.5 - - + -
702B LEU* 2.8 24.6 + - + +
703B SER* 3.9 6.1 - - - +
705B SER* 1.3 71.0 - - - +
707B ASP* 1.3 68.8 + - - +
709B PHE* 3.1 6.3 + - - +
710B LYS* 2.9 42.3 + - + +
769B LEU* 3.8 28.3 - - + -
773B LEU* 3.9 15.9 - - + -
800B LEU* 5.3 4.0 - - + -
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Residues in contact with ASP 707 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703B SER 3.0 19.0 + - - +
704B LEU* 4.0 4.3 - - - +
706B VAL* 1.3 79.7 - - - +
708B ALA* 1.3 62.5 + - - +
710B LYS* 3.2 6.7 + - - +
711B ILE* 3.0 30.3 + - - +
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Residues in contact with ALA 708 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704B LEU 3.0 19.7 + - - +
705B SER* 3.7 7.4 - - - +
707B ASP* 1.3 77.3 + - - +
709B PHE* 1.3 62.8 + - - +
711B ILE* 3.4 22.4 + - - +
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Residues in contact with PHE 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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705B SER 3.0 18.4 + - - +
706B VAL* 3.1 5.4 + - - +
708B ALA* 1.3 78.3 - - - +
710B LYS* 1.3 61.2 + - + +
711B ILE 3.5 2.3 + - - -
772B LEU* 5.2 0.2 - - + -
773B LEU* 3.6 27.4 - - + -
776B PHE* 3.4 43.5 - + - -
777B ASN* 5.7 1.8 - - - -
793B ALA* 3.6 24.2 - - + -
794B CYS 4.6 1.1 - - - -
795B SER* 3.3 45.0 + - - -
796B GLN* 4.4 0.2 - - - +
800B LEU* 3.7 35.4 - - + -
801B LEU 4.9 0.4 - - - -
802B LEU* 4.2 10.8 - - + -
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Residues in contact with LYS 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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958A GLU* 5.0 9.9 - - + +
959A ARG* 5.1 11.9 - - - -
706B VAL* 2.9 36.0 + - + +
707B ASP* 3.8 6.5 - - - +
709B PHE* 1.3 77.6 - - + +
711B ILE* 1.3 57.3 + - - +
795B SER 4.0 20.0 - - - +
796B GLN* 3.0 25.1 + - - +
800B LEU* 4.1 18.4 - - + -
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Residues in contact with ILE 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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707B ASP* 3.0 23.8 + - - +
708B ALA* 3.4 14.6 - - - +
709B PHE 3.3 3.3 - - - -
710B LYS* 1.3 79.6 - - - +
796B GLN* 4.9 3.4 - - - -
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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