Contacts of the helix formed by residues 96 - 100 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ASP* 4.9 0.7 - - - -
292B ARG* 4.9 0.7 + - - -
61C PHE* 4.0 42.3 - + + -
92C ASN* 4.7 0.8 + - - -
94C PHE 3.7 1.4 - - - +
95C THR* 1.3 83.2 - - - +
97C PRO* 1.3 73.1 - - + +
98C VAL* 3.0 48.7 - - + +
99C PHE* 2.8 39.0 + - + +
100C LYS 4.1 0.2 + - - -
118C LYS* 6.2 0.2 - - - -
362D VAL* 3.9 22.4 - - + +
363D ASP* 4.2 13.3 + - - -
366D ALA* 4.7 3.6 - - + +
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Residues in contact with PRO 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B ASP* 4.0 20.2 - - + +
29B ALA 3.2 26.9 - - - +
30B THR* 4.0 13.7 - - + -
292B ARG* 4.2 11.4 - - - +
95C THR 3.6 4.3 - - - +
96C HIS* 1.3 98.0 - - + +
98C VAL* 1.3 61.6 + - - +
99C PHE 3.0 0.2 - - - -
100C LYS* 3.0 28.0 + - - +
366D ALA* 3.6 18.4 - - + +
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Residues in contact with VAL 98 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96C HIS* 2.9 28.3 + - + -
97C PRO* 1.3 77.0 - - - +
99C PHE* 1.3 89.0 + - + +
100C LYS* 3.3 5.5 + - - +
101C ASP* 4.8 1.2 + - - +
102C GLY 4.3 0.5 - - - +
111C VAL* 3.7 23.5 - - + +
114C TYR* 4.3 9.4 - - + -
360D PHE* 3.9 18.6 - - + -
362D VAL* 3.9 10.3 - - + +
365D ALA* 3.8 29.2 - - + +
366D ALA* 3.5 10.2 - - - +
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Residues in contact with PHE 99 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B ARG* 4.9 0.2 - - - -
61C PHE* 6.0 0.2 - + - -
92C ASN 4.2 3.1 - - - -
93C LEU* 3.4 55.2 - - + +
94C PHE* 4.1 4.9 - - - -
96C HIS* 2.8 23.8 + - + +
98C VAL* 1.3 93.0 - - + +
100C LYS* 1.3 57.4 + - - +
101C ASP 3.1 3.1 - - - -
102C GLY 2.8 36.6 + - - +
103C ALA* 3.8 7.9 - - + -
111C VAL* 4.0 11.9 - - + -
114C TYR* 3.6 34.5 - + - -
115C ALA* 4.0 19.7 - - + -
118C LYS* 4.2 13.2 - - + -
140C ARG* 3.1 15.0 - - - +
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Residues in contact with LYS 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B THR* 4.3 9.4 - - + -
292B ARG* 3.4 48.1 + - - +
293B THR* 3.4 44.7 - - + +
294B GLU 5.8 0.4 - - - -
96C HIS 4.1 0.4 + - - -
97C PRO 3.0 16.4 + - - +
98C VAL 3.3 3.5 + - - +
99C PHE* 1.3 77.2 - - - +
101C ASP* 1.3 60.1 + - + +
102C GLY 3.4 0.4 - - - -
108C ASP* 5.9 0.4 + - - -
140C ARG* 4.3 3.6 + - - -
188C ARG* 3.5 12.8 + - - -
334D ARG* 5.4 0.2 - - - +
365D ALA 3.5 7.1 + - - -
366D ALA* 2.9 30.4 + - - +
368D ARG 2.8 28.7 + - - -
369D GLY* 4.6 0.9 - - - -
370D MET* 4.0 12.9 - - + -
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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