Contacts of the strand formed by residues 296 - 304 (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 VAL 296 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286A ILE* 5.0 5.4 - - - +
287A LYS* 3.3 27.1 + - + +
288A LEU* 4.1 2.7 - - - -
289A TYR* 3.8 19.7 - - + +
294A GLU 3.4 11.2 - - - +
295A PRO* 1.3 80.1 - - - +
297A LYS* 1.3 63.3 + - - +
298A THR* 3.8 6.8 + - - -
295B TYR* 3.3 22.1 - - + -
296B CYS* 3.0 42.4 - - - +
297B LEU* 5.1 1.6 - - - +
298B ASN* 4.7 0.4 - - - -
305B VAL* 4.8 5.8 - - + -
310B ILE* 5.1 4.0 - - + -
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Residues in contact with LYS 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A VAL* 1.3 89.5 - - - +
298A THR* 1.3 80.7 + - - +
299A LYS* 4.1 15.8 + - + +
294B VAL 4.1 0.2 - - - +
295B TYR* 3.9 2.8 - - - -
296B CYS* 3.5 23.5 + - - +
298B ASN* 3.5 30.6 - - - +
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Residues in contact with THR 298 (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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287A LYS* 5.2 2.5 + - - +
296A VAL 3.8 5.2 + - - -
297A LYS* 1.3 97.8 + - - +
299A LYS* 1.3 65.3 + - - +
300A THR* 4.0 6.4 + - - +
293B THR* 3.2 28.0 - - - +
294B VAL 3.8 7.4 - - - +
295B TYR* 3.8 20.9 - - + -
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Residues in contact with LYS 299 (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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297A LYS* 4.1 15.8 - - + +
298A THR* 1.3 78.2 - - - +
300A THR* 1.3 63.5 + - - +
301A ARG* 4.2 28.2 - - + +
292B GLU 4.1 0.3 - - - +
293B THR* 3.5 2.4 - - - -
294B VAL* 3.4 32.5 + - + +
296B CYS* 5.3 10.5 - - - -
302B GLU* 3.9 27.1 + - - +
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Residues in contact with THR 300 (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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298A THR* 4.0 6.6 + - - +
299A LYS* 1.3 77.1 + - - +
301A ARG* 1.3 68.2 + - - +
302A THR* 4.2 2.9 + - - +
291B LYS* 4.5 30.7 - - + +
292B GLU 4.1 3.8 - - - +
293B THR* 4.2 13.4 + - - +
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Residues in contact with ARG 301 (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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299A LYS* 4.2 28.1 - - + +
300A THR* 1.3 79.0 - - - +
302A THR* 1.3 58.7 + - - +
303A PHE* 3.8 8.7 - - + -
310A LEU* 3.5 39.6 - - + +
290B GLN 3.7 1.6 - - - +
291B LYS* 4.3 0.7 - - - -
292B GLU* 2.7 45.0 + - + +
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Residues in contact with THR 302 (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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300A THR* 4.2 4.0 + - - +
301A ARG* 1.3 72.7 - - - +
303A PHE* 1.3 67.1 + - - +
310A LEU* 2.9 21.4 - - - +
311A LEU* 3.1 25.7 + - + +
316A THR* 5.6 1.8 - - + -
278B VAL* 5.7 2.7 - - + -
289B ILE* 3.4 31.4 - - + -
290B GLN 3.4 11.2 - - - +
291B LYS* 2.9 28.7 - - + +
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Residues in contact with PHE 303 (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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301A ARG* 3.8 12.6 - - + -
302A THR* 1.3 79.0 - - - +
304A ASN* 1.3 69.8 + - - +
305A THR* 3.5 6.5 + - - -
308A GLY* 4.6 7.6 - - - +
309A GLY 2.9 25.4 - - - +
310A LEU* 3.7 8.5 - - + -
311A LEU* 3.6 10.5 - - - -
289B ILE* 3.8 1.2 - - - -
290B GLN* 3.0 47.9 + - + -
292B GLU* 3.7 46.7 - - + -
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Residues in contact with ASN 304 (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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303A PHE* 1.3 73.6 - - - +
305A THR* 1.3 58.5 + - - +
306A SER* 2.5 43.5 + - - -
307A THR* 3.1 22.8 + - - +
308A GLY* 2.9 30.8 + - - -
309A GLY 2.8 9.9 + - - +
311A LEU* 3.5 17.4 - - + +
280B ASP* 3.4 24.7 + - - -
288B ASP* 3.4 22.1 + - - +
289B ILE* 4.7 1.8 - - - +
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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