Contacts of the strand formed by residues 146 - 149 (chain F) in PDB entry 2QJK
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 GLY 146 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137F ILE 4.1 0.5 - - - +
140F VAL* 3.4 11.1 + - - -
141F SER* 3.1 27.7 + - - -
144F PHE 3.2 3.4 - - - -
145F GLY* 1.3 80.4 - - - +
147F TRP* 1.3 76.9 + - - -
156F TYR 3.1 10.2 + - - -
157F ASP 3.6 13.9 - - - -
158F SER 3.9 0.2 - - - -
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Residues in contact with TRP 147 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62F GLN* 2.9 30.2 + - - -
73F PHE* 3.6 23.9 - + + -
75F ARG* 4.1 29.2 - - + -
123F LEU* 3.5 22.0 - - + -
125F MET* 3.4 34.1 - - + -
136F PRO* 3.7 14.6 - - + -
137F ILE 3.0 24.7 - - - +
138F GLY* 3.3 10.3 - - - -
141F SER 3.2 6.5 + - - +
146F GLY* 1.3 81.3 - - - -
148F PHE* 1.3 61.6 + - - +
149F CYS 4.2 0.2 - - - -
154F SER 3.9 0.5 - - - +
155F HIS* 3.7 3.1 - - - +
156F TYR* 3.0 41.2 + - + +
157F ASP 3.4 22.4 - - - -
158F SER* 4.2 5.6 - - - -
160F GLY* 3.9 5.4 - - - -
171F LEU* 5.0 1.8 - - + -
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Residues in contact with PHE 148 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384A GLN* 6.2 2.2 - - - -
385A THR* 4.3 8.7 - - - -
1B ALA 6.1 3.4 - - - -
136F PRO* 4.0 1.1 - - - -
137F ILE* 2.8 38.8 + - + +
141F SER* 3.5 12.7 + - - +
142F GLY* 4.1 14.6 - - - +
147F TRP* 1.3 74.7 - - - +
149F CYS* 1.3 62.7 + - - +
150F PRO* 3.2 28.1 - - + +
153F GLY* 3.3 36.6 - - - -
154F SER 3.4 9.6 - - - -
155F HIS* 3.7 26.7 - + - -
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Residues in contact with CYS 149 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F CYS* 3.6 21.5 - - + -
134F CYS* 3.6 24.5 - - - -
136F PRO* 3.9 12.8 - - + +
148F PHE* 1.3 72.5 - - - +
150F PRO* 1.3 59.8 - - - +
151F CYS* 3.0 7.1 + - - -
153F GLY* 3.0 24.8 + - - -
154F SER* 2.9 19.2 + - - +
156F TYR* 4.7 1.3 - - + -
200F FES 2.2 39.5 - - - -
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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