Contacts of the helix formed by residues 96 - 100 (chain F) in PDB entry 4HHM
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 HIS 96 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362E VAL* 3.4 26.4 + - + +
363E ASP* 4.2 9.0 + - - -
56F ASP* 5.7 3.0 + - - +
61F PHE* 3.4 45.8 - + + -
92F ASN* 4.6 1.2 + - - -
94F PHE 3.6 3.5 - - - +
95F THR* 1.3 82.7 - - - +
97F PRO* 1.3 76.4 - - + +
98F VAL* 3.0 51.4 + - + -
99F PHE* 3.1 28.8 + - + +
118F LYS* 6.3 0.9 - - - -
28G ASP* 5.3 1.6 - - - -
292G ARG* 4.8 0.2 + - - -
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Residues in contact with PRO 97 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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366E ALA* 3.8 15.9 - - + +
95F THR 3.4 4.0 - - - +
96F HIS* 1.3 97.7 - - + +
98F VAL* 1.3 63.8 + - - +
99F PHE 3.0 2.7 - - - -
100F LYS* 3.0 29.3 + - - +
28G ASP* 4.8 7.9 - - + +
29G ALA 3.7 16.6 - - - +
30G THR* 3.4 33.2 - - + -
292G ARG* 4.1 6.5 - - - +
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Residues in contact with VAL 98 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360E PHE* 4.1 26.9 - - + -
362E VAL* 3.9 13.9 - - + +
365E ALA* 4.3 10.0 - - + -
366E ALA* 3.5 14.2 - - + +
96F HIS* 3.0 28.3 + - + -
97F PRO* 1.3 79.1 - - - +
99F PHE* 1.3 90.4 + - + +
100F LYS* 3.3 6.0 + - - +
101F ASP* 4.8 1.4 + - - +
102F GLY 4.4 0.5 - - - +
111F VAL* 3.5 26.5 - - + +
114F TYR* 4.4 8.3 - - + -
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Residues in contact with PHE 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61F PHE* 6.3 0.2 - + - -
92F ASN* 4.2 2.7 - - - -
93F LEU* 3.6 54.7 - - + +
94F PHE* 4.0 4.3 - - - -
96F HIS* 3.1 22.3 + - + +
97F PRO 3.0 0.8 - - - -
98F VAL* 1.3 96.1 - - + +
100F LYS* 1.3 55.4 + - - -
101F ASP 2.9 5.8 - - - -
102F GLY 2.8 36.6 + - - +
103F ALA* 4.0 6.7 - - + -
111F VAL* 3.8 17.3 - - + -
114F TYR* 3.6 32.1 - + - -
115F ALA* 4.0 17.3 - - + -
118F LYS* 4.1 13.7 - - + -
140F ARG* 3.1 13.9 - - - +
292G ARG* 4.9 0.4 - - - -
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Residues in contact with LYS 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334E ARG* 5.5 0.4 - - - +
365E ALA 3.6 6.1 + - - -
366E ALA* 2.9 33.4 + - - +
368E ARG 3.1 26.6 + - - -
369E GLY* 4.8 0.2 - - - -
370E MET* 4.1 10.4 - - - -
97F PRO 3.0 14.4 + - - +
98F VAL 4.8 4.5 + - - +
99F PHE* 1.3 77.0 - - - +
101F ASP* 1.3 61.4 + - + +
102F GLY 3.5 0.2 - - - -
108F ASP* 5.9 0.2 + - - -
140F ARG* 4.4 1.4 + - - +
188F ARG* 3.8 14.9 + - - -
30G THR* 4.1 11.2 - - + -
292G ARG* 3.4 48.3 + - - +
293G THR* 3.0 44.4 - - + +
294G GLU 5.9 0.4 - - - -
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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