Contacts of the strand formed by residues 195 - 201 (chain B) in PDB entry 3DLX
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 GLN 195 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158B PRO* 3.1 22.4 - - - +
161B TYR* 6.4 0.2 - - + -
191B GLU* 3.2 5.9 - - - +
192B PHE 3.1 26.2 + - - +
193B ASN 3.1 7.7 + - - +
194B GLY* 1.3 76.1 - - - +
196B HIS* 1.3 75.6 + - - +
197B PHE* 3.4 24.7 - - + -
431B SER 3.0 26.1 + - - +
432B SER* 5.1 0.7 - - - +
433B ALA* 4.1 22.4 + - - +
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Residues in contact with HIS 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158B PRO* 3.9 9.0 - - - +
161B TYR* 3.6 54.1 + + + +
189B VAL* 4.2 17.5 - - + -
190B ARG 3.6 1.8 - - - -
191B GLU* 3.8 34.7 + - + +
194B GLY 4.4 6.5 + - - -
195B GLN* 1.3 86.6 + - - +
197B PHE* 1.3 65.9 + - - +
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Residues in contact with PHE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A GLY 4.3 3.8 - - - -
153A PRO* 3.5 29.6 - - + -
156B TYR* 4.0 18.6 - - + -
157B THR 3.5 5.6 - - - +
158B PRO* 3.4 41.5 - - + -
161B TYR* 4.9 0.4 - - - -
189B VAL* 3.3 7.0 - - - +
190B ARG 2.8 35.7 + - - +
192B PHE* 3.5 37.2 - + + -
195B GLN* 3.4 40.6 - - + -
196B HIS* 1.3 75.2 - - - +
198B ILE* 1.3 64.3 + - - +
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Residues in contact with ILE 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B PHE 3.6 0.7 - - - +
156B TYR* 3.2 7.3 - - - -
157B THR* 2.9 45.6 + - + +
159B THR 3.2 23.8 - - - +
160B GLY* 3.8 16.4 - - - +
161B TYR* 4.1 15.5 - - + -
165B VAL* 4.1 17.0 - - + -
166B GLN* 3.9 27.8 - - + +
187B ARG* 3.9 17.0 - - + -
188B GLU 3.1 11.0 - - - +
189B VAL* 4.5 3.1 - - - -
197B PHE* 1.3 77.8 - - - +
199B LEU* 1.3 60.8 + - - +
200B GLU* 3.7 6.1 + - + +
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Residues in contact with LEU 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A TYR* 4.2 7.4 - - + -
190A ARG* 3.7 22.4 - - - +
192A PHE* 4.8 3.4 - - + -
154B ALA* 3.7 29.2 - - + -
155B PHE 3.4 21.3 - - - +
156B TYR* 3.7 30.9 - - + +
187B ARG* 3.7 24.4 - - - +
188B GLU* 2.9 42.8 + - + +
198B ILE* 1.3 71.7 - - - +
200B GLU* 1.3 60.8 + - - +
201B GLU* 5.4 5.4 - - + +
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Residues in contact with GLU 200 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136B THR* 4.8 0.7 + - - -
140B THR* 3.4 28.1 + - + +
144B ARG* 3.8 15.8 + - - -
154B ALA* 3.1 5.5 - - - +
155B PHE* 3.0 53.9 + - + +
157B THR* 3.8 18.8 - - + +
159B THR 4.9 0.3 - - - +
165B VAL* 3.7 19.9 - - - +
187B ARG* 3.0 40.5 + - - +
198B ILE* 3.7 5.8 + - + +
199B LEU* 1.3 74.4 - - - +
201B GLU* 1.3 61.7 + - - +
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Residues in contact with GLU 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A PHE* 3.8 25.1 - - + -
193A ASN* 5.3 5.5 + - - +
144B ARG* 2.7 37.3 + - - +
153B PRO 3.4 9.9 - - - +
154B ALA* 4.5 5.8 - - + -
155B PHE* 5.1 0.7 - - - -
199B LEU* 5.4 5.4 - - + +
200B GLU* 1.3 81.7 + - - +
202B ALA* 1.3 66.5 + - - +
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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