Contacts of the helix formed by residues 625 - 629 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146P ARG* 3.4 31.5 + - - +
543P LYS 3.2 21.1 - - - +
545P PRO* 3.3 32.8 - - + -
621P VAL* 2.9 20.4 - - + +
624P ASP* 1.3 82.6 - - - +
626P ASN* 1.3 62.0 + - - +
627P LYS 3.3 0.2 - - - -
628P LEU* 3.0 24.2 - - + +
629P GLN* 4.7 3.5 - - - +
645P LEU* 3.8 20.0 - - + -
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Residues in contact with ASN 626 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D C 2.7 32.3 + - - +
146P ARG* 5.3 0.2 - - - +
529P GLU* 4.8 5.9 + - - +
530P TYR* 3.6 34.4 + - - -
543P LYS* 5.2 7.5 + - - +
624P ASP* 2.8 22.8 + - - +
625P PRO* 1.3 74.6 - - - +
627P LYS* 1.3 49.6 + - - +
628P LEU 2.7 5.1 + - - -
629P GLN* 2.6 37.6 + - - +
630P TYR* 3.3 10.8 - - + -
666P GTP 2.9 18.1 + - - +
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Residues in contact with LYS 627 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524P ASN* 3.2 28.1 + - - +
558P TYR* 5.7 1.3 - - - -
620P GLU* 3.9 31.4 + - - +
621P VAL* 5.1 2.5 - - + -
624P ASP* 3.0 32.2 + - - +
626P ASN* 1.3 76.8 - - - +
628P LEU* 1.3 56.3 + - - +
629P GLN 3.0 1.8 - - - -
630P TYR* 3.2 32.2 + - + +
631P LYS* 3.0 38.2 + - + +
632P TRP* 3.0 42.9 + - + -
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Residues in contact with LEU 628 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146P ARG* 5.9 1.6 - - - -
621P VAL* 4.1 22.1 - - + +
624P ASP 4.4 0.2 + - - -
625P PRO* 3.0 17.4 + - + +
626P ASN 2.7 0.8 + - - -
627P LYS* 1.3 78.6 - - - +
629P GLN* 1.3 69.6 + - + +
630P TYR 3.5 0.7 - - - -
632P TRP* 3.2 19.5 - - + +
633P THR* 4.4 16.1 - - - -
634P GLU 4.4 0.4 - - - +
637P VAL* 3.8 28.9 - - + -
642P HIS* 4.2 27.8 - - + +
645P LEU* 4.2 14.4 - - + -
646P MET* 4.4 18.2 - - + -
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Residues in contact with GLN 629 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D C 3.1 70.8 + - + +
146P ARG* 5.2 10.5 - - - +
399P ASP* 6.1 1.6 - - - +
451P LYS* 5.7 0.2 - - - -
625P PRO 4.7 5.2 - - - +
626P ASN* 2.6 15.1 + - - +
628P LEU* 1.3 92.2 + - - +
630P TYR* 1.3 59.4 + - + +
632P TRP 5.1 0.2 - - - -
646P MET* 4.4 23.2 - - - +
666P GTP 2.8 17.3 + - - +
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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