Contacts of the strand formed by residues 195 - 201 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A GOL 4.8 4.6 + - - -
158A PRO* 3.3 28.3 - - - +
161A TYR* 6.5 0.2 - - + -
191A GLU* 3.2 2.6 - - - -
192A PHE 2.9 31.4 + - - +
193A ASN 3.2 3.7 + - - +
194A GLY* 1.3 78.5 - - - +
196A HIS* 1.3 73.1 + - - +
197A PHE* 3.3 27.3 - - + -
431A SER 3.7 14.6 + - - -
432A SER* 6.1 0.2 - - - -
433A ALA* 5.0 14.3 + - - +
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Residues in contact with HIS 196 (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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158A PRO* 4.1 6.2 - - - +
161A TYR* 3.6 42.7 + - + +
189A VAL* 3.6 22.7 - - + -
190A ARG 3.7 1.1 - - - -
191A GLU* 4.0 23.6 - - + +
194A GLY 4.9 2.9 + - - -
195A GLN* 1.3 86.4 + - - +
197A PHE* 1.3 66.9 + - - +
161C TYR* 2.6 29.5 + - - -
196C HIS* 3.3 41.3 + + - -
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Residues in contact with PHE 197 (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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156A TYR* 3.9 16.8 - - + -
157A THR 3.4 7.9 - - - +
158A PRO* 3.4 40.6 - - + -
161A TYR* 5.2 0.4 - - - -
189A VAL* 3.3 6.8 - - - +
190A ARG 2.9 32.5 + - - +
192A PHE* 3.6 34.3 - + + -
195A GLN* 3.3 44.9 - - + -
196A HIS* 1.3 73.1 - - - +
198A ILE* 1.3 66.3 + - - +
151B GLY 4.1 3.6 - - - -
153B PRO* 3.3 35.0 - - + -
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Residues in contact with ILE 198 (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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156A TYR* 3.3 5.0 - - - -
157A THR* 2.8 44.9 + - + +
159A THR 3.3 22.7 - - - +
160A GLY 4.0 8.1 - - - -
161A TYR* 4.4 9.9 - - + +
165A VAL* 4.0 12.6 - - + -
166A GLN* 3.4 31.6 - - + -
187A ARG* 3.9 19.3 - - + -
188A GLU 3.2 5.8 - - - +
189A VAL* 3.7 8.5 - - + -
197A PHE* 1.3 80.7 - - - +
199A LEU* 1.3 61.7 + - - +
200A GLU* 3.7 23.7 + - - +
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Residues in contact with LEU 199 (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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154A ALA* 3.9 27.4 - - + -
155A PHE 3.6 13.2 - - - +
156A TYR* 3.4 43.1 - - + +
187A ARG* 3.6 23.6 - - - +
188A GLU* 3.0 40.1 + - + +
198A ILE* 1.3 71.8 - - - +
200A GLU* 1.3 59.5 + - - +
201A GLU* 5.0 7.5 - - + +
156B TYR* 4.1 7.9 - - + -
190B ARG* 3.8 19.7 - - - +
192B PHE* 4.5 3.4 - - + -
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Residues in contact with GLU 200 (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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136A THR* 6.0 0.2 - - - -
137A PRO* 5.3 0.5 - - - +
140A THR* 3.4 26.8 + - + +
144A ARG* 3.7 26.7 + - - -
154A ALA* 3.2 4.3 - - - +
155A PHE* 2.9 53.5 + - + +
157A THR* 3.6 20.1 - - + +
159A THR 4.9 0.3 - - - +
165A VAL* 4.0 9.2 - - - +
187A ARG* 3.5 31.1 + - - -
198A ILE* 3.7 16.7 - - + +
199A LEU* 1.3 73.0 - - - +
201A GLU* 1.3 63.0 + - - +
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Residues in contact with GLU 201 (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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144A ARG* 2.7 43.1 + - - +
153A PRO 3.4 10.6 - - - +
154A ALA* 4.4 7.0 - - + -
155A PHE* 5.1 1.1 - - - -
199A LEU* 5.0 7.0 - - + +
200A GLU* 1.3 77.3 + - - +
202A ALA* 1.3 66.8 - - - +
192B PHE* 3.5 25.9 - - + -
193B ASN* 4.6 8.7 - - - +
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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