Contacts of the strand formed by residues 300 - 305 (chain B) in PDB entry 1JRX
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 300 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B GLU* 5.4 4.5 - - - -
295B LYS* 4.3 6.7 - - - -
296B GLY* 2.7 39.9 + - - -
297B MET 4.7 0.4 - - - -
298B TYR 3.5 2.0 - - - -
299B LYS* 1.3 78.6 - - - +
301B TYR* 1.3 64.8 + - - -
302B TYR* 3.6 6.4 + - - -
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Residues in contact with TYR 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B LEU* 3.5 17.8 - - - +
111B ASP* 2.6 44.0 + - + +
114B GLU* 3.6 33.3 + - + +
115B ARG* 3.5 27.1 - - + -
118B ALA* 3.8 23.9 - - + +
279B ILE* 4.2 13.7 - - + -
293B LEU* 4.3 7.6 - - + -
294B VAL 3.4 15.3 - - - -
295B LYS* 3.5 34.9 - - + +
299B LYS 4.5 3.3 - - - +
300B GLY* 1.3 71.8 - - - -
302B TYR* 1.3 63.4 + - - +
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Residues in contact with TYR 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B ASP* 3.8 21.2 + - - -
118B ALA* 4.2 9.9 - - - -
124B HIS* 3.3 39.5 - + + +
125B ASP* 3.9 1.8 - - - -
155B ILE* 5.1 1.2 - - - +
273B ARG* 2.7 47.5 + - - -
276B THR* 3.8 10.1 - - + +
293B LEU* 3.5 3.2 - - - +
294B VAL* 2.7 59.2 + - + +
296B GLY 4.6 2.0 - - - -
299B LYS* 5.0 8.7 - - + -
300B GLY 3.8 13.9 - - - -
301B TYR* 1.3 75.9 - - - +
303B TRP* 1.3 59.2 + - - +
304B VAL* 3.7 13.8 - - + +
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Residues in contact with TRP 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ALA 3.2 22.8 + - - -
119B LEU* 3.6 21.8 + - + -
121B SER 2.8 22.8 + - - -
122B ALA 4.1 2.2 + - - -
123B PRO* 3.4 41.1 - - + +
124B HIS 2.8 26.7 + - - +
282B LEU* 3.4 31.9 - - + -
290B LYS* 4.1 23.6 - - + -
292B ILE 3.2 11.4 - - - +
293B LEU* 3.9 4.5 - - - -
294B VAL 4.5 0.2 - - - +
302B TYR* 1.3 78.3 - - - +
304B VAL* 1.3 81.3 + - - +
305B LYS* 3.5 29.2 - - + -
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Residues in contact with VAL 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125B ASP* 3.3 31.6 - - + +
127B VAL* 3.7 20.0 - - + -
130B VAL* 3.5 30.3 - - + -
153B ILE* 3.7 16.6 - - + -
155B ILE* 6.2 1.3 - - + -
273B ARG* 4.6 1.1 - - - +
291B GLY* 3.0 4.0 - - - -
292B ILE* 2.8 36.5 + - + +
294B VAL* 5.1 7.0 - - + -
302B TYR* 3.7 14.1 - - + +
303B TRP* 1.3 82.1 - - - +
305B LYS* 1.3 63.4 + - - +
306B ALA* 4.6 0.3 - - - +
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Residues in contact with LYS 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B PRO* 3.7 13.9 - - + +
125B ASP 2.7 8.9 + - - -
126B THR* 3.2 33.6 - - + +
127B VAL 2.9 25.1 + - - +
290B LYS* 3.4 22.8 + - - +
303B TRP* 3.5 20.4 - - + -
304B VAL* 1.3 76.0 - - - +
306B ALA* 1.3 63.9 + - - +
307B ASP* 5.9 1.2 + - - -
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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