Contacts of the strand formed by residues 145 - 149 (chain D) in PDB entry 1C2O
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 VAL 145 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D VAL* 4.1 4.9 - - + -
102D TRP 3.5 11.2 - - - +
103D THR* 3.9 13.2 - - + +
104D PRO* 4.9 0.7 - - + -
108D PRO* 4.5 5.2 - - + -
112D THR* 3.5 11.3 - - + +
113D PRO 3.4 6.0 + - - +
114D VAL* 3.1 37.1 - - + +
115D LEU 3.1 4.1 + - - -
144D ALA* 1.3 72.7 - - - +
146D LEU* 1.3 60.3 + - - +
147D VAL* 4.7 0.4 - - + -
187D ILE* 3.5 31.9 - - + -
190D PHE* 3.9 9.2 - - + +
191D GLY 3.8 11.2 - - - +
192D GLY* 3.7 23.1 - - - +
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Residues in contact with LEU 146 (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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101D VAL* 3.3 4.5 - - - +
102D TRP* 2.9 63.3 + - + +
115D LEU* 3.5 18.2 - - + +
117D TRP* 5.0 2.2 - - + -
133D TYR 5.2 0.2 - - - +
135D GLY* 3.4 36.1 - - - +
138D LEU* 3.9 23.1 - - + -
139D ALA* 5.1 0.2 - - + -
144D ALA* 3.4 6.4 + - + +
145D VAL* 1.3 74.2 - - - +
147D VAL* 1.3 74.7 + - - +
148D SER* 4.3 4.9 - - - +
200D PHE* 4.8 6.3 - - + -
455D PHE* 3.9 20.2 - - + -
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Residues in contact with VAL 147 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99D LEU* 4.0 22.2 - - + -
100D ASN 3.1 17.5 - - - +
101D VAL* 4.1 4.0 - - + -
114D VAL* 5.1 2.0 - - + -
115D LEU 3.0 6.5 + - - +
116D ILE* 3.2 18.2 - - + +
117D TRP* 2.7 33.6 + - - +
145D VAL* 4.7 3.8 - - + +
146D LEU* 1.3 82.1 - - - +
148D SER* 1.3 60.0 + - - +
149D MET* 4.3 2.5 - - + +
179D ALA* 5.9 1.8 - - + +
183D VAL* 3.6 30.7 - - + -
187D ILE* 3.7 19.7 - - + -
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Residues in contact with SER 148 (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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99D LEU* 4.3 1.1 - - - -
100D ASN* 2.8 44.3 + - - -
102D TRP* 3.5 18.5 - - - -
117D TRP* 3.8 29.4 - - - -
128D ALA* 3.2 22.9 + - - +
133D TYR 4.6 3.6 + - - -
146D LEU* 4.5 2.7 - - - -
147D VAL* 1.3 76.9 - - - +
149D MET* 1.3 60.6 + - - +
455D PHE* 6.2 0.2 - - - -
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Residues in contact with MET 149 (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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37D PHE* 3.9 3.4 - - + -
98D TYR 3.7 2.2 - - - +
99D LEU* 3.6 23.1 - - + -
116D ILE* 4.6 5.4 - - + -
117D TRP 3.8 15.2 - - - +
118D ILE* 4.2 20.9 - - + -
119D TYR* 3.3 20.6 - - - -
128D ALA* 3.6 2.6 - - - +
147D VAL* 4.8 2.5 - - + +
148D SER* 1.3 73.9 - - - +
150D ASN* 1.3 77.7 + - - +
151D TYR* 4.5 2.9 - - + +
176D GLN* 3.3 49.6 - - + +
179D ALA* 3.7 23.6 - - + -
180D LEU* 4.4 10.3 - - + -
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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