Contacts of the strand formed by residues 193 - 196 (chain D) in PDB entry 2QLR
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 PHE 193 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125D PHE* 3.9 22.0 - + - -
128D ILE* 4.0 25.1 - - + -
129D ILE* 3.6 33.7 - - + -
134D ASN 4.6 0.8 + - - -
135D VAL* 3.4 33.4 - - + +
136D LEU* 3.1 28.8 + - - +
149D LEU* 4.5 4.3 - - + -
191D PRO* 3.5 1.3 - - - +
192D LYS* 1.3 86.4 - - + +
194D LEU* 1.3 61.4 + - - +
195D TYR* 3.7 31.9 - - + -
225D PHE* 4.1 6.1 - - - -
226D LEU* 3.0 25.4 - - + +
228D ILE* 4.3 11.2 - - + -
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Residues in contact with LEU 194 (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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136D LEU* 3.1 38.4 - - + +
137D LEU* 3.8 4.9 - - - -
138D ASP 5.2 0.7 - - - +
159D VAL* 4.3 7.9 - - + -
166D ILE* 5.0 11.2 - - + -
171D LEU* 3.4 42.2 - - + -
193D PHE* 1.3 74.6 - - - +
195D TYR* 1.3 67.7 + - - +
196D THR* 5.1 7.2 - - + -
216D ILE* 3.7 16.8 - - + -
225D PHE* 3.8 17.7 - - + -
226D LEU 2.8 9.6 + - - +
227D ILE* 3.4 14.4 - - + +
228D ILE 2.7 31.7 + - - -
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Residues in contact with TYR 195 (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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121D LEU* 4.0 5.8 - - + -
125D PHE* 3.7 23.6 - + + -
136D LEU 2.7 13.0 + - - +
137D LEU* 3.1 44.5 - - + +
138D ASP* 3.9 1.4 - - - +
141D ALA* 5.6 6.7 - - + -
142D TYR* 4.7 1.6 - - - +
145D THR* 3.1 32.6 - - + +
149D LEU* 5.7 1.1 - - + -
193D PHE* 3.7 21.0 - - + -
194D LEU* 1.3 76.4 - - - +
196D THR* 1.3 69.4 + - - +
197D VAL* 3.2 18.5 - - + +
228D ILE* 3.5 23.8 - - + -
230D ASP* 2.5 44.0 + - + -
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Residues in contact with THR 196 (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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138D ASP* 3.2 22.0 + - - -
166D ILE* 4.3 10.1 - - + +
194D LEU* 5.1 6.5 - - + -
195D TYR* 1.3 85.0 - - - +
197D VAL* 1.3 71.2 + - - +
198D PRO* 3.9 6.4 - - + +
208D LEU* 4.1 14.2 - - + +
216D ILE* 6.4 0.2 - - + -
227D ILE* 4.9 6.3 - - + -
228D ILE 3.3 8.3 + - - +
229D GLU* 3.8 1.2 - - - -
230D ASP* 2.8 30.7 + - - +
246D PHE* 4.0 28.3 - - + -
428D GOL 4.3 1.9 + - - -
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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