Contacts of the helix formed by residues 625 - 629 (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 PRO 625 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146R ARG* 3.4 32.6 + - - +
543R LYS 3.2 21.3 - - - +
545R PRO* 3.3 31.9 - - + -
621R VAL* 2.9 20.4 - - + +
624R ASP* 1.3 83.1 - - - +
626R ASN* 1.3 62.1 + - - +
627R LYS 3.3 0.4 - - - -
628R LEU* 3.0 23.6 - - + +
629R GLN* 4.7 3.3 - - - +
645R LEU* 3.8 19.5 - - + -
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Residues in contact with ASN 626 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6F C 2.7 32.2 + - - +
146R ARG* 5.3 0.4 - - - +
529R GLU* 4.8 5.7 + - - +
530R TYR* 3.6 34.8 + - - -
543R LYS* 5.2 7.0 + - - +
624R ASP* 2.8 22.0 + - - +
625R PRO* 1.3 75.3 - - - +
627R LYS* 1.3 49.9 + - - +
628R LEU 2.7 5.3 + - - -
629R GLN* 2.6 38.2 + - - +
630R TYR* 3.3 11.0 - - + -
666R GTP 2.9 18.4 + - + +
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Residues in contact with LYS 627 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
524R ASN* 3.2 28.0 + - - +
558R TYR* 5.7 1.8 - - - -
620R GLU* 3.9 32.3 + - - +
621R VAL* 5.1 1.8 - - + -
624R ASP* 3.0 33.0 + - - +
626R ASN* 1.3 76.8 - - - +
628R LEU* 1.3 55.6 + - - +
629R GLN 3.0 1.6 - - - -
630R TYR* 3.2 31.1 + - + +
631R LYS* 3.0 38.4 + - + +
632R TRP* 3.0 42.3 + - + -
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Residues in contact with LEU 628 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146R ARG* 5.9 1.3 - - - -
621R VAL* 4.1 23.2 - - + +
624R ASP 4.4 0.2 + - - -
625R PRO* 3.0 17.6 + - + +
626R ASN 2.7 1.0 + - - -
627R LYS* 1.3 78.8 - - - +
629R GLN* 1.3 67.9 + - + +
630R TYR 3.5 1.1 - - - -
632R TRP* 3.2 20.1 - - + +
633R THR* 4.4 14.9 - - - -
634R GLU 4.4 1.5 + - - +
637R VAL* 3.8 29.6 - - + -
642R HIS* 4.2 28.3 - - + +
645R LEU* 4.2 14.6 - - + -
646R MET* 4.4 18.2 - - + -
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Residues in contact with GLN 629 (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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6F C 3.1 70.6 + - + +
146R ARG* 5.2 10.3 - - - +
399R ASP* 6.1 1.2 - - - +
451R LYS* 5.6 0.4 - - - -
625R PRO 4.7 5.2 - - - +
626R ASN* 2.6 16.0 + - - +
628R LEU* 1.3 90.1 + - - +
630R TYR* 1.3 59.3 + - + +
646R MET* 4.4 22.6 - - - +
666R GTP 2.8 18.1 + - - +
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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