Contacts of the helix formed by residues 538 - 542 (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 ASP 538 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147P LYS* 5.8 0.5 - - - +
536P VAL* 3.3 13.2 - - + +
537P ARG* 1.3 76.5 - - - +
539P ARG* 1.3 58.4 + - - +
540P SER* 2.5 33.1 + - - -
541P LYS* 2.9 49.8 + - + +
542P ARG 3.6 1.0 + - - -
601P TYR* 3.5 11.6 - - - -
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Residues in contact with ARG 539 (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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41P GLU* 5.3 9.7 + - - -
537P ARG 3.3 3.1 + - - +
538P ASP* 1.3 72.9 - - - +
540P SER* 1.3 62.0 + - - +
541P LYS 3.0 1.3 + - - -
542P ARG* 3.1 51.6 + - - +
545P PRO* 3.1 48.1 + - - +
546P PHE* 3.7 18.0 - - + -
547P PRO* 4.5 4.4 - - - +
594P ASP* 2.8 31.5 + - - -
597P GLU* 3.5 34.6 + - - +
601P TYR* 3.1 23.0 + - + +
47Q ASP* 5.3 1.6 + - - -
49Q ARG* 4.3 10.5 - - - +
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Residues in contact with SER 540 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146P ARG* 2.5 32.0 + - - -
147P LYS* 3.7 21.1 + - - +
538P ASP* 2.5 27.3 + - - -
539P ARG* 1.3 77.4 - - - +
541P LYS* 1.3 53.7 + - - +
545P PRO* 4.6 1.8 - - - -
546P PHE* 5.3 0.6 - - - -
601P TYR* 3.9 10.9 - - - -
644P VAL* 3.1 39.5 - - - -
645P LEU* 4.2 6.5 - - - +
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Residues in contact with LYS 541 (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* 4.4 2.3 + - - -
147P LYS* 4.0 16.1 - - + +
148P GLY* 3.7 29.8 - - - +
158P ASN* 3.6 35.1 + - + +
159P ASP* 4.7 4.2 - - - +
160P MET* 5.4 4.3 - - - +
533P GLN* 4.7 3.1 + - - -
536P VAL* 4.2 12.2 - - + +
538P ASP* 2.9 36.6 + - + +
540P SER* 1.3 80.3 + - - +
542P ARG* 1.3 62.8 + - - +
543P LYS* 5.4 3.5 - - - +
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Residues in contact with ARG 542 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41P GLU* 6.4 0.6 - - - +
146P ARG* 3.8 11.1 + - - -
532P VAL* 3.4 22.4 + - - +
533P GLN* 3.0 25.6 + - + +
534P SER* 3.4 24.8 + - - +
536P VAL* 2.8 42.7 + - + -
537P ARG* 4.8 2.6 + - - +
538P ASP 3.8 3.8 - - - +
539P ARG* 3.1 61.4 + - - +
541P LYS* 1.3 81.8 - - - +
543P LYS* 1.3 65.7 + - - +
544P ARG 3.3 13.6 + - - +
545P PRO* 3.6 17.4 + - - +
547P PRO* 5.7 1.2 - - - +
48Q PRO* 5.7 2.0 - - - +
49Q ARG* 6.1 1.2 - - - +
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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