Contacts of the strand formed by residues 98 - 102 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A VAL* 5.7 3.8 - - + -
204A VAL* 4.1 16.6 - - + -
211A ILE* 4.0 21.4 - - + +
214A THR* 4.3 9.9 - - - +
97D TRP* 1.3 73.3 - - - +
99D VAL* 1.3 67.1 + - - +
100D TYR* 3.2 0.7 + - - -
446D PHE* 3.2 4.7 - - - -
447D CYS 3.1 27.5 + - - +
448D GLY 4.7 0.2 + - - -
449D VAL* 4.2 15.0 - - + -
453D THR* 4.0 6.7 - - + +
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Residues in contact with VAL 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A SER* 4.9 3.5 + - - -
176A VAL* 4.1 25.0 - - + +
195A SER* 4.5 15.3 - - - -
202A VAL* 5.8 7.4 - - + -
204A VAL* 4.1 29.6 - - + +
206A LYS* 4.9 1.7 - - - -
211A ILE* 4.2 0.9 - - - +
97D TRP 4.2 0.2 + - - -
98D ALA* 1.3 71.8 - - - +
100D TYR* 1.3 61.2 + - - +
101D SER 4.9 3.1 - - - +
102D LYS* 6.2 0.4 - - + -
444D ILE* 6.0 0.9 - - + -
445D SER 4.3 2.2 - - - +
446D PHE* 3.4 32.9 - - + -
458D TRP* 3.7 41.3 - - + +
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Residues in contact with TYR 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A PHE* 3.4 7.1 - - - -
175A SER* 4.5 1.0 - - - -
176A VAL* 4.4 3.2 - - - +
206A LYS* 3.0 35.5 + - - +
209A GLY 3.0 27.7 + - - -
210A ILE* 4.5 6.9 - - - +
211A ILE* 3.9 21.5 - - + -
98D ALA 3.2 1.3 + - - +
99D VAL* 1.3 75.2 - - - +
101D SER* 1.3 65.7 + - - +
122D ILE* 5.2 0.2 - - + -
129D CYS* 3.9 23.9 - - - +
163D VAL* 4.3 23.0 - - + +
410D PHE* 4.4 17.0 - + - -
412D GLN* 4.2 15.7 + - - -
445D SER* 2.6 36.3 + - - +
446D PHE* 4.0 9.6 - - - -
447D CYS* 3.8 12.3 - - - -
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Residues in contact with SER 101 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A PHE* 3.5 20.6 - - - -
176A VAL* 3.6 7.4 - - - +
99D VAL* 3.9 2.5 - - - +
100D TYR* 1.3 87.2 - - - +
102D LYS* 1.3 64.2 + - - +
122D ILE* 4.4 7.4 - - - +
163D VAL* 4.5 3.3 - - - +
164D GLY* 4.2 17.4 + - - -
443D SER* 5.5 1.7 + - - -
444D ILE* 3.2 6.8 - - - +
445D SER* 2.5 46.6 + - - +
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Residues in contact with LYS 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A PRO 3.4 21.8 - - - +
155A HIS* 3.3 16.7 - - - -
157A THR* 3.9 12.0 + - + +
173A PHE* 3.4 22.3 - - - -
176A VAL* 4.0 12.6 - - + -
99D VAL* 6.2 0.2 - - + -
101D SER* 1.3 79.4 - - - +
103D ASP* 1.3 62.2 + - - +
104D ASN* 2.6 39.3 - - - +
164D GLY* 3.7 4.0 - - - +
426D LEU* 4.9 2.0 - - - +
442D SER* 5.7 2.0 - - - -
443D SER 3.5 7.4 - - - +
444D ILE* 3.5 16.6 - - + +
458D TRP* 4.1 18.4 - - + -
459D PRO 2.9 29.2 + - - -
460D ASP* 3.5 7.7 + - - +
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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