Contacts of the strand formed by residues 123 - 128 (chain D) in PDB entry 3KHU
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 TYR 123 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2D PHE* 3.8 46.8 - + + -
82D ALA 4.7 1.6 - - - +
83D ASP* 4.7 6.9 - - - +
121D ASN 3.7 0.9 + - - +
122D GLY* 1.3 70.3 - - - -
124D LYS* 1.3 74.0 + - - +
125D ILE* 3.6 29.3 - - + +
153D ASN* 3.3 35.9 - - + -
155D GLN* 3.8 19.8 - - + +
187D GLU* 4.3 10.8 + - - -
190D ARG* 4.2 23.1 + - - -
191D ALA* 3.9 17.5 + - - +
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Residues in contact with LYS 124 (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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79D ILE 3.2 18.4 + - - +
80D LYS 2.9 23.7 + - - -
81D GLU 4.2 0.8 - - - -
82D ALA 2.6 28.1 + - - +
83D ASP 3.4 11.0 - - - +
85D VAL* 4.2 13.0 - - + -
116D ILE* 5.4 0.7 - - + -
120D SER* 3.4 35.7 - - - +
121D ASN 4.1 15.0 + - - +
122D GLY 4.1 0.6 + - - -
123D TYR* 1.3 82.9 + - - +
125D ILE* 1.3 67.5 + - - +
126D VAL* 4.1 2.2 - - + -
153D ASN 3.2 6.8 + - - +
154D LEU* 3.4 19.7 - - + -
155D GLN* 2.9 27.0 + - - +
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Residues in contact with ILE 125 (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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2D PHE* 4.1 15.3 - - + -
4D ILE* 4.1 10.3 - - + -
83D ASP 3.0 7.4 + - - +
84D LEU* 3.2 24.3 - - + +
85D VAL* 2.7 32.4 + - - +
123D TYR* 3.6 26.5 - - + +
124D LYS* 1.3 75.0 - - - +
126D VAL* 1.3 57.3 + - - +
127D THR* 3.7 2.0 - - - +
155D GLN* 3.5 5.8 - - + +
157D LEU* 3.7 30.1 - - + -
191D ALA* 4.0 13.5 - - + +
194D ALA* 3.8 29.2 - - + -
195D LEU* 5.7 0.4 - - + -
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Residues in contact with VAL 126 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D VAL* 3.3 14.8 - - + +
87D ILE* 3.8 28.0 - - + -
116D ILE* 3.9 25.4 - - + -
124D LYS* 4.9 0.9 - - + -
125D ILE* 1.3 76.2 - - - +
127D THR* 1.3 63.7 + - - +
128D GLU 5.4 0.2 - - - +
140D ILE* 4.7 5.8 - - + -
144D PHE* 3.9 34.3 - - + -
154D LEU* 4.4 13.2 - - + -
155D GLN 2.6 13.9 + - - +
156D VAL* 3.2 6.8 - - + +
157D LEU 2.8 24.8 + - - +
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Residues in contact with THR 127 (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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84D LEU* 3.2 22.7 - - - +
85D VAL 2.9 9.1 + - - -
86D PHE* 3.3 28.0 - - + -
87D ILE* 2.8 27.3 + - - -
125D ILE* 3.7 2.1 - - - +
126D VAL* 1.3 75.2 - - - +
128D GLU* 1.3 65.9 + - - +
129D LYS 3.4 0.5 + - - -
157D LEU* 3.3 20.2 - - - +
158D SER 4.2 0.9 - - - -
159D ASN* 3.3 36.1 - - + +
195D LEU* 4.1 6.7 - - + +
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Residues in contact with GLU 128 (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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87D ILE* 3.8 10.3 - - + -
109D ILE* 5.9 2.0 - - + -
126D VAL* 4.3 0.6 - - + +
127D THR* 1.3 70.8 - - - +
129D LYS* 1.3 58.8 + - - +
130D SER 4.4 2.0 - - - +
132D VAL* 3.7 21.8 - - + +
136D ALA* 3.0 16.5 - - - +
137D ALA* 3.0 31.2 + - + +
140D ILE* 3.6 23.2 - - + +
156D VAL* 5.2 1.1 - - + -
157D LEU 3.0 11.4 + - - +
158D SER* 3.6 13.0 + - - -
159D ASN* 2.8 29.5 + - - +
160D PRO* 4.3 0.7 - - - +
217D GLU* 2.7 28.8 - - - +
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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