Contacts of the helix formed by residues 645 - 653 (chain B) in PDB entry 4RIB
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 PRO 645 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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643B ASN 3.2 5.6 - - - +
644B HIS* 1.3 98.0 - - + +
646B SER* 1.3 62.6 + - - +
647B LEU 3.1 1.9 + - - -
648B ARG* 3.1 27.0 + - + +
649B CYS* 4.1 5.6 - - - -
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Residues in contact with SER 646 (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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597B GLN* 3.6 27.1 - - - -
601B ASP* 3.7 20.9 + - - -
604B ARG* 4.2 4.5 + - - -
644B HIS* 2.9 32.4 + - - +
645B PRO* 1.3 78.6 - - - +
647B LEU* 1.3 65.5 + - - +
648B ARG 3.3 0.6 + - - -
649B CYS* 3.4 8.9 - - - -
650B HIS* 3.2 29.4 + - - -
662B VAL* 5.3 1.4 - - - +
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Residues in contact with LEU 647 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638B TRP* 4.1 27.4 - - + -
641B LEU* 3.7 26.2 - - + +
642B LYS* 4.2 6.3 - - + -
643B ASN 4.1 7.0 - - - +
644B HIS* 3.7 7.0 - - + +
645B PRO 3.1 1.2 + - - -
646B SER* 1.3 78.7 - - - +
648B ARG* 1.3 83.4 + - - +
649B CYS 3.3 0.2 - - - -
650B HIS* 3.3 20.1 + - + +
651B GLU* 2.9 36.4 + - - +
662B VAL* 4.1 15.9 - - + -
663B GLY 4.6 0.2 - - - +
699B TYR* 4.1 17.5 - - - +
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Residues in contact with ARG 648 (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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643B ASN* 2.8 40.7 + - - +
644B HIS 3.2 8.8 + - - -
645B PRO* 3.1 17.8 + - + +
647B LEU* 1.3 103.4 - - - +
649B CYS* 1.3 66.0 + - - +
651B GLU* 3.7 26.5 + - - +
652B ASP* 3.6 21.7 + - - +
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Residues in contact with CYS 649 (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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597B GLN* 3.2 44.6 - - - +
645B PRO 4.1 6.5 - - - -
646B SER* 3.4 14.4 - - - -
648B ARG* 1.3 74.7 - - - +
650B HIS* 1.3 67.9 + - - +
652B ASP* 3.2 15.8 + - - +
653B LEU* 3.2 15.6 + - - +
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Residues in contact with HIS 650 (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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595B ILE 3.8 15.5 + - - -
596B PHE* 5.4 1.0 - - - -
597B GLN* 4.5 6.5 + - - -
601B ASP* 2.9 39.5 + - - -
646B SER* 3.2 27.0 + - - -
647B LEU* 3.3 22.0 + - - +
648B ARG 3.3 0.2 - - - -
649B CYS* 1.3 74.0 - - + +
651B GLU* 1.3 60.2 + - - +
652B ASP 2.8 10.4 + - - -
653B LEU* 2.9 26.7 + - + +
658B ARG* 3.7 11.5 - - - +
661B THR* 3.8 33.3 - - + +
662B VAL* 4.1 13.6 - - + +
699B TYR* 4.3 10.5 - - - +
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Residues in contact with GLU 651 (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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647B LEU* 2.9 23.4 + - + +
648B ARG* 3.9 30.9 + - - +
649B CYS 3.5 0.2 - - - -
650B HIS* 1.3 70.0 - - - +
652B ASP* 1.3 61.8 + - - +
658B ARG* 3.7 22.1 + - - +
698B ILE* 4.3 43.2 - - + +
699B TYR* 4.8 6.4 + - + +
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Residues in contact with ASP 652 (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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648B ARG 3.6 11.5 + - - +
649B CYS* 3.4 12.1 - - - +
650B HIS 2.8 0.6 + - - -
651B GLU* 1.3 79.3 - - - +
653B LEU* 1.3 66.9 + - - +
654B PRO* 3.7 1.6 - - - +
658B ARG* 5.1 0.2 - - - -
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Residues in contact with LEU 653 (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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593B THR* 4.0 20.6 - - + -
594B HIS 4.2 6.7 - - - +
595B ILE* 4.2 22.0 - - - +
649B CYS 3.2 11.3 + - - +
650B HIS* 2.9 19.5 + - + +
652B ASP* 1.3 77.8 - - - +
654B PRO* 1.3 83.2 - - + +
657B LEU* 3.7 32.5 - - + +
658B ARG* 3.0 32.9 + - - +
661B THR* 4.0 27.6 - - + -
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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