Contacts of the strand formed by residues 98 - 102 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204E VAL* 4.1 15.7 - - + -
211E ILE* 3.8 22.7 - - + +
214E THR* 4.5 8.5 - - - +
97H TRP* 1.3 75.2 - - - +
99H VAL* 1.3 65.9 + - - +
100H TYR 3.2 0.2 + - - -
446H PHE* 3.2 6.5 - - - -
447H CYS 3.1 28.9 + - - +
448H GLY 4.5 0.2 + - - -
449H VAL* 4.1 18.6 - - + -
453H THR* 4.6 4.0 - - + -
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Residues in contact with VAL 99 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E SER* 4.8 2.9 + - - -
176E VAL* 3.6 31.7 - - + +
195E SER* 4.7 10.8 - - - -
202E VAL* 5.8 6.7 - - + -
204E VAL* 4.0 26.2 - - + +
206E LYS* 4.6 1.6 - - - -
211E ILE* 4.1 5.0 - - - +
97H TRP 4.3 0.6 + - - +
98H ALA* 1.3 71.1 - - - +
100H TYR* 1.3 63.2 + - - +
101H SER 4.8 2.9 - - - +
102H LYS* 6.0 0.2 - - + -
444H ILE* 6.1 0.9 - - + -
445H SER 4.4 1.8 - - - +
446H PHE* 3.5 28.0 - - + -
458H TRP* 3.5 45.5 - - + +
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Residues in contact with TYR 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E PHE* 3.3 9.5 - - - -
175E SER* 4.3 1.4 - - - -
176E VAL* 4.3 3.6 - - - +
206E LYS* 2.9 45.1 + - - +
209E GLY 2.8 28.6 + - - -
210E ILE* 4.5 5.8 - - - +
211E ILE* 3.8 21.3 - - + -
98H ALA 3.2 2.2 + - - +
99H VAL* 1.3 74.2 - - - +
101H SER* 1.3 63.8 + - - +
122H ILE* 5.4 1.3 - - + -
129H CYS* 4.1 21.7 - - + +
163H VAL* 4.5 20.6 - - + +
410H PHE* 4.3 14.8 - + - -
412H GLN* 4.2 19.8 + - - -
445H SER* 2.7 37.8 + - - +
446H PHE* 4.0 8.3 - - - -
447H CYS* 4.1 6.1 - - - -
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Residues in contact with SER 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E PHE* 3.6 19.1 - - - -
176E VAL* 3.7 6.4 - - - +
99H VAL* 3.9 2.1 - - - +
100H TYR* 1.3 87.5 - - - +
102H LYS* 1.3 63.9 + - - +
103H ASP 5.3 0.3 + - - -
122H ILE* 4.4 7.4 - - - +
163H VAL* 4.6 4.5 - - - +
164H GLY* 4.1 18.8 + - - -
443H SER* 5.4 1.9 + - - -
444H ILE* 3.2 7.8 - - - +
445H SER* 2.8 44.7 + - - +
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Residues in contact with LYS 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154E PRO 3.3 27.4 - - - +
155E HIS* 3.3 9.4 - - - -
157E THR* 3.8 12.3 + - + +
173E PHE* 3.5 21.6 - - - -
176E VAL* 4.0 13.9 - - + -
99H VAL* 6.0 0.2 - - + -
101H SER* 1.3 77.6 - - - +
103H ASP* 1.3 63.8 + - - +
104H ASN* 2.7 37.2 - - - +
164H GLY* 3.7 4.0 - - - +
426H LEU* 5.1 0.8 - - - +
442H SER* 5.5 1.2 + - - -
443H SER 3.6 7.0 - - - +
444H ILE* 3.5 17.4 - - + +
458H TRP* 4.0 19.5 - - + -
459H PRO 2.9 29.2 + - - -
460H ASP* 3.2 10.5 + - - +
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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