Contacts of the strand formed by residues 257 - 262 (chain A) in PDB entry 1JEQ
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 SER 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A ALA* 3.1 6.9 - - - +
256A LEU* 1.3 88.2 - - - +
258A ARG* 1.3 75.2 + - - +
259A LEU* 3.9 14.7 - - - +
272A GLY* 3.4 1.9 - - - -
273A ILE* 2.9 39.1 + - - +
400A TYR* 5.6 1.2 + - - -
402A PRO* 6.1 0.5 - - - +
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Residues in contact with ARG 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255A ALA* 4.5 14.9 - - + +
257A SER* 1.3 83.3 - - - +
259A LEU* 1.3 70.5 + - - +
271A VAL 3.2 12.3 - - - +
272A GLY* 4.5 2.5 - - - -
371A GLU* 2.8 32.4 + - + +
373A SER* 4.3 9.7 + - - -
374A LEU* 4.1 29.7 - - + +
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Residues in contact with LEU 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A SER* 3.9 16.2 - - - +
258A ARG* 1.3 84.1 - - - +
260A LYS* 1.3 67.6 + - - +
261A LEU 3.6 0.3 + - - -
270A SER* 3.4 7.7 - - - -
271A VAL* 2.9 39.0 + - + +
273A ILE* 3.9 20.8 - - + +
343A PRO* 4.4 6.7 - - + -
344A GLY* 4.0 28.9 - - - +
345A LEU* 4.5 4.0 - - + +
374A LEU* 6.4 0.7 - - - -
400A TYR* 3.9 24.5 - - + +
401A THR 4.4 2.9 - - - +
402A PRO* 3.6 22.7 - - + +
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Residues in contact with LYS 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A LEU* 1.3 76.5 - - - +
261A LEU* 1.3 59.2 + - - +
262A LYS* 3.3 29.7 + - - +
268A VAL* 3.7 22.4 - - + -
269A ILE 3.7 5.2 - - - -
270A SER* 4.8 2.0 - - - +
343A PRO 5.1 3.8 + - - +
344A GLY* 3.4 6.6 - - - -
345A LEU 3.0 23.0 + - - -
541B GLU* 6.0 1.8 - - - -
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A LEU 3.6 1.2 + - - -
260A LYS* 1.3 71.6 - - - +
262A LYS* 1.3 60.4 - - - +
263A LEU* 3.5 29.8 + - + +
268A VAL* 3.9 0.2 - - - -
269A ILE* 2.8 51.6 + - + +
271A VAL* 4.0 23.6 - - + -
345A LEU* 3.6 27.4 - - + +
347A LEU* 5.2 4.3 - - + -
368A VAL* 5.0 3.1 - - + -
382A PHE* 5.4 3.1 - - + -
385A LEU* 5.8 3.1 - - + -
398A CYS* 5.5 4.5 - - - -
413A LEU* 4.4 21.8 - - + -
432A PHE* 6.3 1.6 - - + -
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Residues in contact with LYS 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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260A LYS* 4.0 35.6 - - + +
261A LEU* 1.3 74.3 - - - +
263A LEU* 1.3 61.6 + - - +
264A ASN* 3.4 19.0 + - - +
265A LYS* 4.8 6.5 - - - +
267A ILE 3.7 4.3 - - - -
268A VAL* 3.5 19.3 - - + -
342A ASP* 4.5 18.0 + - - +
343A PRO 3.8 17.3 + - - -
344A GLY* 5.3 1.5 - - - -
345A LEU 3.3 8.8 + - - +
346A MET* 4.0 21.4 - - + +
347A LEU* 3.1 26.3 + - - +
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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