Contacts of the strand formed by residues 135 - 140 (chain D) in PDB entry 3RMD
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 135 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D GLU* 3.2 45.9 + - + +
133D ILE* 3.2 11.9 + - - +
134D ASP* 1.3 80.7 - - - +
136D ILE* 1.3 71.6 + - - +
149D PHE 3.6 11.9 + - - -
150D ASP* 4.8 0.4 - - - +
320D TYR* 3.8 9.0 - - + -
321D ILE* 3.9 16.4 - - + -
324D ASN* 4.3 3.6 - - + +
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Residues in contact with ILE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D PHE* 4.9 1.8 - - + -
114D ASP 3.5 13.2 - - - +
115D ILE* 4.1 18.2 - - + +
133D ILE* 5.4 2.5 - - + +
135D ALA* 1.3 83.6 - - - +
137D THR* 1.3 65.8 + - - +
138D HIS 4.4 3.6 - - - +
147D TYR 3.7 0.9 - - - +
148D VAL* 3.4 3.2 - - - +
149D PHE* 2.8 61.0 + - + +
197D LEU* 4.2 14.1 - - + -
201D TYR* 3.2 56.1 - - + +
226D VAL* 5.8 1.6 - - + -
324D ASN* 3.8 4.3 - - - +
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Residues in contact with THR 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D PHE* 3.4 11.0 - - - -
114D ASP 2.9 10.4 + - - -
136D ILE* 1.3 74.7 - - - +
138D HIS* 1.3 59.3 + - - +
139D TYR 3.7 0.2 + - - -
146D PHE* 4.2 20.9 - - + -
147D TYR 3.3 5.4 - - - +
148D VAL* 3.3 32.3 - - + +
324D ASN* 2.2 28.2 + - - -
325D ILE* 3.7 12.4 - - + +
328D VAL* 3.1 39.1 - - + +
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Residues in contact with HIS 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111D ALA* 3.0 30.2 - - + +
113D PHE* 3.7 12.0 - + + +
136D ILE* 4.0 2.0 - - + +
137D THR* 1.3 72.0 - - - +
139D TYR* 1.3 74.4 + - - +
140D ASP* 4.8 4.4 + - - +
147D TYR* 2.8 38.3 + - - +
149D PHE* 4.9 1.1 - - + -
201D TYR* 3.0 44.0 + - + +
204D PHE* 3.5 27.5 - + + -
205D TRP* 4.5 18.8 - + - -
208D LYS* 5.4 6.5 + - + +
210D PRO* 4.7 8.5 - - + +
213D LEU* 6.6 0.2 - - + -
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Residues in contact with TYR 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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110D VAL 4.7 4.3 - - - -
111D ALA* 3.2 24.6 - - - -
112D ASN* 3.3 23.3 + - + +
137D THR 3.7 0.4 + - - -
138D HIS* 1.3 77.7 - - - +
140D ASP* 1.3 82.0 + - - +
141D SER* 3.9 12.2 + - - -
144D ASP* 3.1 23.2 + - - -
145D ARG 3.3 26.2 - - - +
146D PHE* 3.5 46.7 - + + +
328D VAL* 3.9 11.2 - - + -
332D LEU* 3.5 29.8 - - + +
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Residues in contact with ASP 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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109D ARG* 3.3 40.3 + - - +
110D VAL 4.4 0.9 - - - -
111D ALA* 4.8 3.1 - - - +
138D HIS* 4.1 7.8 + - + +
139D TYR* 1.3 89.3 - - - +
141D SER* 1.3 77.2 + - - +
142D ILE* 2.6 28.4 + - - +
143D ASP* 3.6 20.5 - - + +
144D ASP* 3.1 18.7 + - - -
145D ARG 3.1 8.5 + - - +
147D TYR* 4.6 6.5 - - + -
204D PHE* 5.5 0.2 - - + -
208D LYS* 3.8 10.2 - - + +
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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
------------------------------------------------------------
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