Contacts of the strand formed by residues 98 - 102 (chain F) in PDB entry 2HU4
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 ALA 98 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97F TRP* 1.3 74.0 - - - +
99F VAL* 1.3 66.4 + - - +
100F TYR* 4.2 0.3 - - - -
446F PHE* 3.0 5.5 - - - -
447F CYS 2.9 37.2 + - - +
448F GLY 4.0 0.2 + - - -
449F VAL* 4.1 15.0 - - + -
453F THR* 3.9 5.8 - - + +
204H VAL* 4.3 14.1 - - + -
211H ILE* 4.0 18.9 - - + +
214H THR* 4.4 9.4 - - + +
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Residues in contact with VAL 99 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97F TRP 4.2 0.4 + - - +
98F ALA* 1.3 73.2 - - - +
100F TYR* 1.3 61.8 + - - +
101F SER 4.9 3.4 - - - +
444F ILE* 6.0 0.9 - - + -
445F SER 4.3 2.5 - - - +
446F PHE* 3.4 27.6 - - + -
458F TRP* 3.5 44.6 - - + +
175H SER* 4.8 2.9 + - - -
176H VAL* 3.9 27.0 - - + +
195H SER* 4.8 11.0 - - - -
202H VAL* 5.5 8.5 - - + +
204H VAL* 3.9 32.7 - - + +
206H LYS* 4.7 2.1 - - - -
211H ILE* 4.0 1.4 - - - +
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Residues in contact with TYR 100 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98F ALA 3.3 1.3 + - - +
99F VAL* 1.3 73.5 - - - +
101F SER* 1.3 63.0 + - - +
122F ILE* 5.4 0.2 - - + -
129F CYS* 4.1 23.2 - - + +
163F VAL* 4.6 21.9 - - + +
410F PHE* 4.2 18.8 - + - -
412F GLN* 4.6 12.3 + - - -
445F SER* 2.8 36.3 + - - +
446F PHE* 3.9 10.1 - - - +
447F CYS* 4.2 6.3 - - - +
173H PHE* 3.4 7.6 - - - -
175H SER* 4.5 1.0 - - - -
176H VAL* 4.4 4.0 - - - +
206H LYS* 2.9 46.7 + - - +
209H GLY 2.8 30.6 + - - -
210H ILE* 4.6 5.9 - - - +
211H ILE* 3.8 19.7 - - + -
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Residues in contact with SER 101 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F VAL* 4.9 2.6 - - - +
100F TYR* 1.3 87.1 - - - +
102F LYS* 1.3 65.0 + - - +
122F ILE* 4.3 6.8 - - - +
163F VAL* 4.6 4.2 - - - +
164F GLY* 4.1 18.4 + - - -
443F SER* 5.5 1.2 + - - -
444F ILE* 3.1 7.9 - - - +
445F SER* 2.6 46.2 + - - +
173H PHE* 3.5 20.0 - - - -
176H VAL* 3.7 7.0 - - - +
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Residues in contact with LYS 102 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99F VAL* 6.2 0.2 - - + -
101F SER* 1.3 78.3 - - - +
103F ASP* 1.3 62.6 + - - +
104F ASN* 2.9 37.0 - - - +
164F GLY* 3.6 3.9 - - - +
426F LEU* 4.9 1.2 - - - +
442F SER* 5.7 1.8 - - - -
443F SER 3.5 7.0 - - - +
444F ILE* 3.5 16.9 - - + +
458F TRP* 3.9 19.3 - - + -
459F PRO 2.8 29.9 + - - -
460F ASP* 3.0 13.3 + - - +
154H PRO 3.6 21.1 - - - +
155H HIS* 3.7 11.3 - - - -
157H THR* 3.9 11.7 - - + +
173H PHE* 3.3 22.6 - - - -
176H VAL* 4.0 12.8 - - + -
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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