Contacts of the strand formed by residues 134 - 142 (chain D) in PDB entry 3U8M
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 134 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124D ASP 3.7 5.8 - - - +
125D VAL* 3.4 23.6 - - - +
126D SER 3.2 21.8 - - - +
127D GLY 3.7 2.2 + - - -
128D VAL* 3.7 8.7 - - + +
133D GLY* 1.3 73.2 - - - -
135D THR* 1.3 57.5 + - - +
136D CYS 4.0 0.4 - - - -
199D LEU 3.5 0.7 - - - +
200D ASN* 2.6 22.2 + - - -
201D PHE* 2.7 38.4 + - + -
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Residues in contact with THR 135 (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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124D ASP* 3.5 22.0 + - - +
126D SER 4.8 0.2 + - - -
133D GLY 4.2 0.9 + - - -
134D ALA* 1.3 71.3 - - - +
136D CYS* 1.3 61.6 + - - +
137D ARG* 3.7 5.2 + - + +
198D SER* 3.9 29.2 - - - +
199D LEU 3.2 7.9 - - - +
200D ASN* 3.1 25.4 + - + +
168E TYR* 5.6 0.2 + - - -
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Residues in contact with CYS 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D VAL* 3.8 16.2 - - - -
50D VAL* 5.8 0.2 - - - -
121D PHE* 4.8 0.7 - - - -
123D CYS* 2.0 47.8 - - - -
124D ASP 4.1 4.0 - - - +
134D ALA 4.0 0.6 - - - -
135D THR* 1.3 71.1 - - - +
137D ARG* 1.3 59.5 + - - +
138D ILE* 3.8 18.1 + - - +
197D VAL 3.5 3.1 - - - +
198D SER* 4.6 0.4 - - - -
199D LEU* 2.6 46.6 + - + +
201D PHE* 3.8 22.2 - - + -
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Residues in contact with ARG 137 (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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90D ASN* 2.7 31.4 + - - -
123D CYS* 3.9 7.9 - - + +
124D ASP 5.2 0.2 - - - +
135D THR* 3.7 6.2 + - + +
136D CYS* 1.3 72.5 - - - +
138D ILE* 1.3 56.6 + - - +
139D LYS* 4.1 2.7 + - + +
196D GLU* 3.7 42.6 + - + +
197D VAL 3.6 4.3 - - - +
198D SER* 4.1 17.9 - - - +
167E GLN* 3.8 15.1 + - - -
168E TYR* 3.1 35.9 + - + -
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Residues in contact with ILE 138 (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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33D LEU* 4.4 13.0 - - + -
35D PHE* 4.3 28.5 - - + -
50D VAL* 5.2 2.9 - - + -
52D PHE* 5.6 0.2 - - + -
88D ALA* 4.5 1.1 - - + -
90D ASN* 3.7 3.4 - - - +
121D PHE* 3.6 58.6 - - + -
136D CYS* 4.5 16.2 - - - +
137D ARG* 1.3 78.9 - - - +
139D LYS* 1.3 61.1 + - - +
140D ILE* 3.9 23.9 + - + +
195D VAL 3.6 2.3 - - - +
196D GLU* 3.5 4.1 - - - -
197D VAL* 2.9 43.2 + - + +
199D LEU* 5.6 1.3 - - + -
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Residues in contact with LYS 139 (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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88D ALA* 3.2 4.2 - - - -
89D TYR* 2.7 70.0 + - + +
90D ASN* 3.2 11.4 + - - +
137D ARG* 4.1 3.2 + - + +
138D ILE* 1.3 71.4 - - - +
140D ILE* 1.3 59.2 + - - +
183D VAL* 4.9 7.9 - - - +
185D TYR* 3.0 27.8 + - - -
194D ASP* 3.4 36.9 + - + +
195D VAL 3.6 3.6 - - - -
196D GLU* 4.1 19.5 - - + +
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Residues in contact with ILE 140 (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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31D VAL* 4.5 14.4 - - + +
33D LEU* 3.9 39.3 - - + -
52D PHE* 5.3 2.5 - - + -
54D GLN* 4.0 15.5 - - - +
86D LEU* 4.1 29.6 - - + -
87D ALA 3.3 9.9 - - - +
88D ALA* 4.2 12.3 - - + -
89D TYR* 4.6 0.4 - - - -
138D ILE* 4.0 13.9 - - + +
139D LYS* 1.3 79.5 - - - +
141D GLY* 1.3 61.9 + - - +
152D VAL* 4.7 2.6 - - + +
194D ASP* 3.2 3.9 - - - -
195D VAL* 2.7 43.8 + - + +
197D VAL* 5.4 4.0 - - + -
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Residues in contact with GLY 141 (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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86D LEU* 3.7 9.4 - - - -
87D ALA* 3.0 26.7 + - - +
89D TYR* 4.0 10.8 - - - -
140D ILE* 1.3 79.2 - - - +
142D SER* 1.3 67.7 + - - -
143D TRP* 3.5 0.5 + - - -
152D VAL* 4.5 3.8 - - - -
193D GLU 3.6 15.7 - - - -
194D ASP* 4.1 3.8 - - - -
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Residues in contact with SER 142 (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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85D ASP* 2.8 26.9 + - - -
86D LEU* 3.7 8.7 - - - +
89D TYR* 3.6 13.0 + - - -
141D GLY* 1.3 73.4 - - - -
143D TRP* 1.3 61.4 + - - +
145D HIS* 2.9 38.6 + - - +
150D ILE* 3.9 23.1 - - - -
152D VAL* 4.5 2.6 - - - +
192D TYR* 4.5 11.1 - - - +
193D GLU 3.9 7.1 + - - +
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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