Contacts of the helix formed by residues 638 - 645 (chain R) in PDB entry 1HI0
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 638 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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613R GLU 4.8 4.2 + - - -
614R LEU* 5.2 1.1 - - - -
615R THR* 3.5 10.5 - - - +
618R ASP* 2.5 37.7 + - - -
636R ASP 4.4 0.4 + - - -
637R VAL* 1.3 68.9 - - - +
639R ALA* 1.3 60.3 + - - +
640R ASN* 3.2 16.2 - - - -
641R ILE* 2.8 27.2 + - - +
642R HIS* 2.9 10.9 + - - +
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Residues in contact with ALA 639 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637R VAL 3.2 6.3 + - - -
638R SER* 1.3 70.9 - - - +
640R ASN* 1.3 62.7 + - - +
642R HIS* 3.4 6.9 + - - +
643R GLU* 3.1 32.4 + - - +
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Residues in contact with ASN 640 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602R VAL* 3.6 21.3 - - + +
603R ALA* 6.1 0.7 - - + +
604R SER* 3.1 28.9 + - - +
605R MET* 5.4 1.4 - - - +
613R GLU* 6.1 2.8 - - - +
614R LEU* 4.7 6.9 - - - +
638R SER* 3.3 18.9 - - - -
639R ALA* 1.3 76.4 + - - +
641R ILE* 1.3 70.8 + - - +
643R GLU* 3.8 23.3 + - - +
644R VAL* 3.6 14.6 - - - +
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Residues in contact with ILE 641 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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602R VAL* 3.9 28.5 - - + -
614R LEU* 3.5 34.3 - - + -
618R ASP* 4.3 11.2 - - + +
621R VAL* 5.5 2.0 - - + -
622R LEU* 3.8 35.4 - - + -
637R VAL* 4.1 13.0 - - + -
638R SER* 2.8 19.8 + - - +
640R ASN* 1.3 84.6 - - - +
642R HIS* 1.3 67.4 + - - +
643R GLU 3.1 1.6 - - - -
644R VAL* 2.9 21.4 + - + +
645R LEU* 3.7 9.0 + - + +
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Residues in contact with HIS 642 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144R LYS* 4.2 12.7 - - + -
628R LEU* 4.2 21.0 - - + +
634R GLU* 3.3 63.9 + - + +
637R VAL* 3.7 16.1 - - + +
638R SER 2.9 11.0 + - - +
639R ALA* 3.7 11.7 - - - +
641R ILE* 1.3 76.1 - - - +
643R GLU* 1.3 58.6 + - - +
645R LEU* 3.0 8.6 + - - +
646R MET* 2.8 62.4 + - + +
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Residues in contact with GLU 643 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144R LYS* 6.4 0.2 - - - +
147R LYS* 2.9 19.4 + - - -
639R ALA* 3.1 21.8 + - + +
640R ASN* 3.8 18.6 + - - +
641R ILE 3.1 1.0 - - - -
642R HIS* 1.3 77.0 - - - +
644R VAL* 1.3 55.9 + - + +
646R MET 3.1 16.4 - - - +
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Residues in contact with VAL 644 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147R LYS* 2.8 27.0 + - - +
540R SER* 3.1 23.6 - - - -
546R PHE* 4.7 6.5 - - + -
598R LEU* 5.4 0.7 - - + -
601R TYR* 4.0 33.4 - - + +
602R VAL* 4.2 16.2 - - + -
622R LEU* 4.7 11.7 - - + -
640R ASN 3.6 13.9 - - - +
641R ILE* 2.9 20.5 + - + +
643R GLU* 1.3 78.6 - - - +
645R LEU* 1.3 69.3 + - + +
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Residues in contact with LEU 645 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146R ARG* 3.2 33.9 + - - +
147R LYS* 3.0 29.9 + - - +
540R SER* 4.2 4.7 - - - +
545R PRO* 4.3 9.4 - - + -
621R VAL* 3.5 37.5 - - + +
622R LEU* 4.6 10.8 - - + -
625R PRO* 3.8 22.7 - - + -
628R LEU* 4.2 10.1 - - + -
641R ILE* 4.1 11.0 - - + +
642R HIS* 3.0 6.6 + - - +
644R VAL* 1.3 95.7 - - + +
646R MET* 1.3 65.7 + - + +
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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