Contacts of the strand formed by residues 146 - 149 (chain O) 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 O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138O GLY* 3.9 2.8 - - - -
139O GLY 4.1 0.2 + - - -
140O VAL* 3.4 11.8 + - - +
141O SER 3.4 24.5 + - - -
144O PHE 4.7 0.2 - - - +
145O GLY* 1.3 78.9 - - - +
147O TRP* 1.3 74.8 + - - +
156O TYR 3.1 14.1 + - - -
157O ASP 3.6 12.8 - - - -
158O SER* 3.9 0.4 - - - -
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Residues in contact with TRP 147 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62O GLN* 2.6 34.4 + - - -
73O PHE* 3.6 10.0 - + + -
75O ARG* 4.0 28.7 - - + -
123O LEU* 3.5 30.5 - - + -
125O MET* 3.5 26.9 - - + -
136O PRO* 3.6 24.7 - - + -
137O ILE 3.4 4.9 - - - -
138O GLY* 2.7 28.8 - - - -
139O GLY 4.9 0.7 - - - -
141O SER 3.6 5.0 - - - +
142O GLY* 5.0 0.2 - - - -
146O GLY* 1.3 80.6 - - - -
148O PHE* 1.3 61.3 + - - +
149O CYS 4.2 0.4 - - - -
154O SER 3.9 0.5 - - - +
155O HIS* 3.7 3.5 - - - +
156O TYR* 3.0 40.6 + - + +
157O ASP 3.4 22.0 - - - -
158O SER* 4.2 6.5 - - - -
160O GLY* 3.9 5.6 - - - -
171O LEU* 5.1 2.2 - - + -
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Residues in contact with PHE 148 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136O PRO* 4.0 1.1 - - - -
137O ILE* 2.9 38.0 + - + +
141O SER* 3.8 23.8 + - - +
142O GLY* 4.2 4.9 - - - +
147O TRP* 1.3 76.2 - - - +
149O CYS* 1.3 61.5 + - - +
150O PRO* 3.2 29.6 - - + +
153O GLY* 3.3 35.7 - - - -
154O SER 3.4 11.0 - - - -
155O HIS* 3.7 27.6 - + - -
384P GLN* 6.3 0.7 - - - -
385P THR* 4.6 6.7 - - - -
1Q ALA 5.9 5.8 - - - -
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Residues in contact with CYS 149 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129O CYS* 3.7 15.9 - - + -
134O CYS* 3.6 26.0 - - - -
136O PRO* 3.9 12.7 - - + +
148O PHE* 1.3 72.0 - - - +
150O PRO* 1.3 60.3 - - - +
151O CYS* 3.1 10.9 + - - -
153O GLY* 3.0 25.5 + - - -
154O SER* 2.9 19.2 + - - +
156O TYR* 4.7 1.5 - - + -
200O FES 2.2 39.0 - - - -
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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