Contacts of the strand formed by residues 146 - 149 (chain I) in PDB entry 2QJY
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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I GLY* 4.0 2.8 - - - -
140I VAL* 3.3 9.2 + - - -
141I SER 2.8 31.2 + - - -
144I PHE 3.2 3.8 - - - -
145I GLY* 1.3 79.9 - - - +
147I TRP* 1.3 80.2 + - - -
156I TYR 3.1 10.0 + - - -
157I ASP 3.6 6.1 - - - -
158I SER 3.9 0.2 - - - -
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Residues in contact with TRP 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62I GLN* 2.8 29.8 + - - -
73I PHE* 3.5 24.6 - + + -
75I ARG* 3.8 29.8 - - + -
123I LEU* 3.6 27.8 - - + -
125I MET* 3.6 26.7 - - + -
136I PRO* 3.6 15.9 - - + -
137I ILE 3.0 9.9 - - - +
138I GLY* 3.3 24.9 - - - -
141I SER 3.6 6.4 - - - +
142I GLY* 4.3 1.2 - - - -
146I GLY* 1.3 83.3 - - - -
148I PHE* 1.3 60.7 - - - +
154I SER 4.1 0.2 - - - +
155I HIS* 3.6 2.8 - - - -
156I TYR* 2.9 40.8 + - + +
157I ASP 3.4 22.4 - - - -
158I SER* 4.1 5.8 - - - -
160I GLY* 4.1 4.3 - - - -
171I LEU* 5.1 1.8 - - + -
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Residues in contact with PHE 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I PRO* 4.2 1.8 - - - -
137I ILE* 2.9 36.9 + - + +
141I SER* 3.9 8.1 - - - -
142I GLY* 3.7 17.7 - - - +
147I TRP* 1.3 75.8 - - - +
149I CYS* 1.3 65.7 + - - +
150I PRO* 3.4 30.1 - - + +
153I GLY* 3.8 20.9 - - - -
154I SER 3.6 7.0 - - - -
155I HIS* 3.5 38.4 - + - -
290J ALA 5.7 0.7 - - - -
384J GLN* 6.2 5.6 - - + -
385J THR* 4.3 9.4 - - - -
386J THR* 6.6 0.2 - - + -
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Residues in contact with CYS 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I CYS* 3.6 15.3 - - - -
134I CYS* 3.6 31.0 - - - -
136I PRO* 4.2 12.9 - - + +
148I PHE* 1.3 74.2 - - - +
150I PRO* 1.3 62.5 - - - +
151I CYS 3.2 5.2 - - - -
153I GLY* 3.0 28.4 + - - -
154I SER* 2.8 17.5 + - - +
156I TYR* 4.7 1.1 - - + -
200I FES 2.2 40.6 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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