Contacts of the strand formed by residues 140 - 145 (chain A) in PDB entry 6PUO
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 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ASP* 3.1 4.7 + - - -
130A ILE* 2.9 44.7 + - + +
131A VAL* 6.0 0.2 - - - -
132A PHE* 3.6 29.0 - - + -
136A SER* 4.7 11.3 - - - -
138A LYS* 4.0 29.8 + - - +
139A VAL* 1.3 75.5 - - - +
141A LYS* 1.3 63.6 + - - +
279A SER 3.3 19.5 + - - -
280A ASN* 4.7 3.4 - - - +
281A HIS 3.3 26.0 - - - +
282A SER* 3.8 18.6 - - - +
284A PHE* 4.3 7.0 - - + -
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLY 3.7 7.4 - - - +
129A ASP* 4.3 20.2 - - + -
139A VAL* 5.4 9.0 - - - +
140A LYS* 1.3 77.9 - - - +
142A TYR* 1.3 61.1 + - - +
161A HIS 5.3 1.2 + - - -
162A TRP* 3.6 54.4 + - + +
282A SER 3.8 4.8 + - - -
283A HIS* 3.4 25.7 - - + +
284A PHE* 2.9 23.6 + - - +
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Residues in contact with TYR 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE* 6.1 0.2 - - - +
126A ALA* 3.1 28.8 + - + -
127A PHE 3.4 6.2 + - - -
128A GLY* 2.9 56.2 + - - +
129A ASP 3.4 27.4 - - - -
130A ILE* 4.0 15.5 - - + -
140A LYS 4.6 1.3 - - - +
141A LYS* 1.3 77.9 - - - +
143A VAL* 1.3 66.6 + - - +
162A TRP* 4.0 5.1 + - - -
244A TRP* 5.5 0.9 - + - -
253A LEU* 3.5 50.7 + - + +
259A SER* 4.3 6.9 - - - -
262A ALA* 4.7 0.2 - - - +
284A PHE* 3.1 27.6 - - + +
286A LEU* 4.3 19.3 - - + -
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Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ILE* 4.4 17.0 - - + -
67A ILE* 4.7 11.0 - - + -
124A THR* 5.2 0.9 - - + -
127A PHE* 3.7 26.5 - - + +
142A TYR* 1.3 80.9 - - - +
144A ARG* 1.3 69.4 + - - +
145A VAL* 4.0 17.7 - - + -
154A ILE* 6.4 0.2 - - + -
157A LEU* 4.4 11.4 - - + -
162A TRP* 4.3 14.1 - - + -
284A PHE 3.0 10.8 + - - +
285A ILE* 3.6 14.4 - - + -
286A LEU* 2.9 30.0 + - - +
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ILE* 4.3 2.1 - - - +
69A LYS* 3.4 37.2 - - + +
70A LYS 3.9 10.1 + - - -
93A TYR* 5.2 3.8 + - - -
124A THR* 3.3 25.6 + - + +
125A ASP* 5.5 0.8 - - - +
126A ALA* 3.7 34.5 + - + +
127A PHE* 4.7 1.2 - - - +
143A VAL* 1.3 79.2 - - - +
145A VAL* 1.3 72.2 + - - +
244A TRP* 3.1 51.3 - - + +
254A ILE* 5.2 8.5 - - - +
286A LEU* 3.3 11.7 - - + +
288A ASP* 2.6 34.6 + - + -
290A GLY* 5.8 0.6 - - - -
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Residues in contact with VAL 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A ILE* 4.0 20.2 - - + -
68A LYS 3.7 6.5 - - - -
69A LYS* 5.0 0.9 - - - -
143A VAL* 4.0 20.4 - - + -
144A ARG* 1.3 80.8 - - - +
146A SER* 1.3 71.8 + - - +
149A THR* 4.6 9.6 - - - +
154A ILE* 5.2 13.5 - - + -
285A ILE* 4.3 13.7 - - + -
286A LEU 2.9 7.3 + - - +
287A VAL* 3.8 24.7 - - + -
288A ASP* 2.9 31.0 + - - +
301A LEU* 4.5 7.6 - - + -
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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