Contacts of the strand formed by residues 128 - 134 (chain D) in PDB entry 4KYI
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 VAL 128 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D GLN 3.1 12.8 + - - +
96D ALA* 3.3 1.6 - - + +
97D ALA 2.8 28.7 + - - +
126D ASN* 5.5 4.7 - - - +
127D ILE* 1.3 74.9 - - - +
129D ILE* 1.3 67.0 + - - +
159D LEU* 5.5 4.5 - - + -
178D ILE* 3.9 27.2 - - + +
181D LYS* 4.1 28.7 - - + +
182D LEU* 3.7 28.9 - - + -
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Residues in contact with ILE 129 (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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97D ALA* 3.8 4.9 - - + -
99D VAL* 4.0 26.5 - - + -
116D VAL* 4.2 14.4 - - + +
119D LEU* 3.7 39.7 - - + +
120D GLN* 4.5 8.3 - - + -
127D ILE* 3.8 26.8 + - + +
128D VAL* 1.3 78.3 - - - +
130D ALA* 1.3 64.1 + - - +
158D LEU* 3.6 34.4 - - + +
159D LEU* 3.3 19.9 + - - +
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Residues in contact with ALA 130 (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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97D ALA 3.1 16.0 + - - +
98D ILE* 3.7 4.1 - - - -
99D VAL* 2.9 30.7 + - - +
128D VAL* 5.8 0.2 - - + -
129D ILE* 1.3 78.9 - - - +
131D LEU* 1.3 59.6 + - - +
132D ALA 3.9 0.4 - - - -
158D LEU* 5.0 1.1 - - - -
159D LEU* 3.3 20.9 - - + +
174D ILE* 4.6 14.8 - - + -
178D ILE* 4.1 22.2 - - + -
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Residues in contact with LEU 131 (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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99D VAL* 3.7 17.7 - - + +
101D TYR* 3.7 21.3 - - + -
109D PHE* 4.8 3.1 - - + -
112D ALA* 4.2 16.8 - - + -
116D VAL* 5.3 3.4 - - + -
130D ALA* 1.3 71.7 - - - +
132D ALA* 1.3 57.7 - - - +
149D ALA* 4.1 19.7 - - + +
152D TYR* 4.0 30.1 - - + -
153D ALA* 4.7 3.6 - - + -
158D LEU* 4.8 11.2 - - + -
159D LEU 2.5 15.4 + - - +
160D PHE* 3.2 29.4 - - + -
161D MET 3.1 25.1 + - - -
174D ILE* 4.7 1.5 - - - +
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Residues in contact with ALA 132 (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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37D LEU* 5.1 2.9 - - + -
98D ILE* 3.9 19.3 - - + -
99D VAL 3.0 8.7 + - - +
100D VAL* 3.4 9.4 - - + -
101D TYR* 2.8 34.1 + - - +
130D ALA 3.9 1.0 + - - -
131D LEU* 1.3 73.2 - - - +
133D GLY* 1.3 59.1 + - - +
134D ASN 3.8 0.4 + - - -
161D MET 3.5 4.5 - - - +
163D THR* 4.1 13.7 - - + +
174D ILE* 3.8 22.2 - - + -
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Residues in contact with GLY 133 (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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101D TYR* 3.3 30.9 - - - -
103D ILE* 4.1 8.0 - - - +
131D LEU 4.0 0.2 + - - -
132D ALA* 1.3 70.9 - - - +
134D ASN* 1.3 60.7 + - - +
136D ALA* 4.5 0.7 - - - +
160D PHE* 4.4 1.2 - - - -
161D MET 3.1 12.0 + - - -
162D GLU* 3.5 8.8 - - - +
163D THR* 2.7 30.5 + - - +
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Residues in contact with ASN 134 (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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32D VAL 2.6 29.6 + - - +
33D GLY* 3.2 10.9 + - - -
37D LEU* 3.5 12.1 - - + +
100D VAL* 4.1 12.1 - - + -
101D TYR 2.8 12.4 + - - +
102D ASP* 3.8 0.4 - - - +
103D ILE* 3.4 18.4 + - - +
132D ALA 3.8 1.2 + - - -
133D GLY* 1.3 75.7 - - - +
135D LYS* 1.3 79.8 + - - +
163D THR* 3.2 18.8 + - - +
164D SER* 3.5 1.2 - - - -
165D ALA 3.4 13.0 + - - -
301D GNP 2.9 35.4 + - - +
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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