Contacts of the strand formed by residues 135 - 140 (chain B) in PDB entry 1RD3
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 LYS 135 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A SER* 2.6 108.8 + - + +
133B GLY 3.9 3.4 - - - +
134B TYR* 1.3 74.6 - - - +
136B GLY* 1.3 60.1 + - - +
159B ASN* 4.8 2.5 - - + -
160B LEU 3.2 7.6 - - - +
161B PRO* 3.8 18.4 - - + -
184B TYR* 3.5 26.4 - - - +
186B LYS* 4.4 5.7 - - - -
201B MET* 3.0 18.2 - - - +
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A LEU* 4.4 5.6 - - - -
135B LYS* 1.3 75.5 - - - +
137B ARG* 1.3 60.5 + - - -
159B ASN* 3.2 6.6 - - - +
160B LEU 2.7 32.7 + - - -
199B PHE* 3.4 26.1 - - - -
200B VAL 3.3 11.9 - - - -
201B MET* 3.9 2.2 - - - -
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Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A ARG* 4.0 1.2 - - - +
14A LEU* 2.9 82.6 + - + +
26B MET* 3.4 26.7 + - - +
27B SER* 6.2 1.6 - - - -
136B GLY* 1.3 74.8 - - - -
138B VAL* 1.3 65.3 + - - +
139B THR* 4.2 9.4 - - + -
157B VAL* 3.4 26.5 - - + +
158B VAL 3.5 3.1 - - - -
159B ASN* 3.1 14.9 + - - +
198B PRO 3.4 1.7 - - - +
199B PHE* 3.1 7.3 - - - -
200B VAL* 2.6 55.7 + - + +
207B TRP* 3.5 17.8 - - - -
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Residues in contact with VAL 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.6 20.5 - - + +
137B ARG* 1.3 77.2 - - - +
139B THR* 1.3 69.2 - - - +
157B VAL* 3.3 3.1 - - - +
158B VAL* 2.8 44.4 + - + +
160B LEU* 4.1 9.9 - - + -
190B ALA* 3.9 15.5 - - + -
194B ASP* 5.0 0.4 - - + -
198B PRO 3.6 5.8 - - - +
199B PHE* 3.6 25.6 - - + -
213B VAL* 4.0 16.4 - - + -
228B TYR* 3.8 19.3 - - + +
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 4.3 4.7 - - - -
22B ALA* 5.4 1.6 - - + -
26B MET* 6.0 1.1 - - - -
27B SER* 3.7 18.5 + - - +
30B GLN* 2.4 38.0 + - - +
137B ARG* 4.2 9.0 - - + -
138B VAL* 1.3 86.0 - - - +
140B GLY* 1.3 58.6 + - - +
155B LEU* 4.3 6.5 - - + -
156B GLN 3.1 11.4 - - - +
157B VAL* 3.7 22.9 - - + -
194B ASP* 4.6 2.6 - - - +
197B GLY* 4.3 7.3 - - - -
198B PRO* 3.7 20.2 + - - +
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Residues in contact with GLY 140 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B ILE* 3.9 3.5 - - - +
30B GLN* 4.1 5.8 - - - -
43B GLY* 6.1 2.7 - - - -
139B THR* 1.3 76.2 - - - +
141B TRP* 1.3 59.2 + - - -
142B GLY 3.7 0.3 + - - -
155B LEU* 3.5 14.1 - - - +
156B GLN* 3.1 37.5 + - - +
194B ASP* 3.1 22.2 - - - +
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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