Contacts of the strand formed by residues 125 - 129 (chain D) in PDB entry 4UN7
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 LEU 125 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D TYR* 3.3 11.2 - - - +
122D LEU* 3.7 35.4 - - + +
124D ARG* 1.3 81.7 - - - +
126D ARG* 1.3 60.6 + - - +
164D ASN* 4.0 1.3 + - - +
165D ILE* 2.9 65.0 + - + +
167D LEU* 4.4 12.9 - - + +
170D ARG* 3.8 32.1 - - + +
173D PHE* 3.6 25.6 - - + -
174D VAL* 4.3 9.6 - - + -
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Residues in contact with ARG 126 (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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114D TYR* 3.2 5.4 + - - -
117D GLU 3.9 0.3 - - - +
118D GLY* 3.1 5.4 - - - -
119D ASP* 2.6 58.7 + - + +
124D ARG* 3.8 38.0 - - + +
125D LEU* 1.3 74.7 - - - +
127D ILE* 1.3 64.9 + - - +
128D TRP* 3.5 34.5 - - + -
154D ASP* 5.3 2.9 + - - -
162D VAL* 3.8 15.0 - - + -
163D LEU 3.5 3.6 - - - -
164D ASN* 3.3 24.7 - - - +
7E C 4.4 2.2 - - - +
8E C 4.6 1.2 - - - +
17F C 4.0 5.5 - - - +
18F G 2.8 50.3 + - - -
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Residues in contact with ILE 127 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110D ILE* 5.1 9.6 - - + +
113D LEU* 4.3 23.6 - - + +
114D TYR* 3.6 31.6 - - + +
117D GLU* 3.6 25.1 - - + +
118D GLY* 4.7 0.4 - - - -
126D ARG* 1.3 79.8 - - - +
128D TRP* 1.3 64.6 - - - +
129D ASN 4.1 0.2 + - - -
135D LEU* 4.3 10.3 - - + +
138D VAL* 4.7 17.5 - - + -
142D LEU* 5.4 0.4 - - + -
162D VAL* 3.2 5.9 - - - +
163D LEU* 2.9 50.5 + - + +
165D ILE* 4.3 16.2 - - + -
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Residues in contact with TRP 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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117D GLU* 3.2 55.9 + - - +
118D GLY 4.0 0.2 - - - -
119D ASP* 3.7 24.7 - - + -
126D ARG* 3.5 54.3 - - + +
127D ILE* 1.3 77.4 - - - +
129D ASN* 1.3 65.4 + - - +
154D ASP* 3.1 32.2 + - + -
155D ASP* 6.2 0.2 - - + -
160D VAL* 4.1 8.7 - - + -
161D TYR 3.5 8.1 - - - +
162D VAL* 3.9 18.4 - - + +
15F C 3.7 21.1 - + + -
16F C 3.5 52.2 - + + -
17F C 3.6 11.0 - + - -
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Residues in contact with ASN 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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19D ILE* 4.8 8.5 + - - +
113D LEU* 4.8 4.9 - - - +
117D GLU* 2.9 29.9 + - - +
127D ILE* 4.1 0.8 + - + -
128D TRP* 1.3 72.6 + - - +
130D LYS* 1.3 63.4 + - - +
131D ASN* 3.0 33.6 + - - +
134D LEU* 4.1 19.0 - - - +
135D LEU* 3.8 25.5 - - + +
160D VAL* 3.6 6.2 - - - +
161D TYR* 2.8 32.8 + - - +
15F C 3.7 13.9 + - - -
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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