Contacts of the strand formed by residues 372 - 377 (chain 5) in PDB entry 3J7Y
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 ASN 372 (chain 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1245 THR 3.4 13.5 + - - -
1255 LYS 3.1 18.2 + - - +
1265 THR* 3.2 5.5 - - - -
1275 LYS* 2.9 21.5 + - - +
2485 THR* 5.0 0.3 - - - +
3185 PHE* 4.0 2.6 - - - -
3575 PHE* 3.5 27.7 - - + -
3595 LEU* 3.5 27.6 - - - +
3605 ASN* 2.9 30.0 + - - +
3615 THR* 3.2 19.4 + - - +
3645 LEU* 4.8 1.2 - - - +
3715 LYS* 1.3 82.2 - - - +
3735 LEU* 1.3 62.1 + - - +
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Residues in contact with LEU 373 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1275 LYS* 3.4 19.7 - - + +
1295 ILE* 4.8 3.1 - - + -
2405 ALA* 3.9 2.5 - - + -
2445 GLU* 3.6 37.0 - - + +
2455 ILE* 4.3 8.7 - - + -
2485 THR* 4.3 11.7 - - + -
3585 GLN* 3.5 33.8 + - + +
3605 ASN* 3.2 26.0 - - - +
3715 LYS 4.1 2.9 - - - +
3725 ASN* 1.3 79.0 - - - +
3745 ALA* 1.3 63.6 + - - +
3755 TRP* 3.7 39.0 - - + -
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Residues in contact with ALA 374 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1215 LEU* 5.1 2.9 - - + -
1265 THR* 3.3 7.0 + - - +
1275 LYS 2.7 21.0 + - - +
1285 LEU* 3.4 10.7 - - + -
1295 ILE* 3.1 15.8 + - - +
3145 ILE* 5.0 4.0 - - + -
3555 LEU* 3.8 18.4 - - + -
3565 VAL 3.4 7.9 - - - +
3575 PHE* 3.6 27.9 - - + +
3735 LEU* 1.3 76.1 - - - +
3755 TRP* 1.3 62.1 + - - +
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Residues in contact with TRP 375 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1295 ILE* 3.4 46.7 - - + +
1315 GLY 3.3 22.9 - - - +
1325 LEU* 4.1 4.7 - - + +
1335 PRO* 3.5 30.7 - - + +
2395 ILE* 3.5 34.3 - - + +
2405 ALA* 4.1 13.2 - - + -
2445 GLU* 5.0 2.0 - - - -
3555 LEU* 3.5 1.2 - - - -
3565 VAL* 3.2 55.9 + - + +
3585 GLN* 4.1 7.4 - - + +
3735 LEU* 3.7 41.3 - - + -
3745 ALA* 1.3 71.9 - - - +
3765 VAL* 1.3 67.1 + - - +
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Residues in contact with VAL 376 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1175 VAL* 5.9 0.7 - - + -
1285 LEU* 3.6 37.9 - - + -
1295 ILE 3.2 6.1 + - - +
1305 GLU* 2.9 31.1 - - - +
1325 LEU* 4.8 2.0 - - - -
3105 ARG* 5.2 16.8 - - + +
3135 MET* 5.6 0.4 - - + -
3145 ILE* 4.8 4.9 - - + -
3535 HIS* 6.6 0.2 - - + -
3545 PHE 3.3 11.4 - - - +
3555 LEU* 3.4 32.5 - - + -
3755 TRP* 1.3 72.9 - - - +
3775 ASP* 1.3 67.0 + - - +
3785 SER* 3.8 13.8 + - - +
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Residues in contact with ASP 377 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1305 GLU 3.9 2.7 - - - +
1315 GLY* 3.4 5.7 - - - -
1325 LEU* 2.8 45.4 + - + +
1375 LEU* 5.6 1.7 - - - +
3525 PHE 3.8 1.6 - - - +
3545 PHE* 3.2 45.9 + - + +
3765 VAL* 1.3 75.5 - - - +
3785 SER* 1.3 64.8 + - - +
3795 ASP 3.5 1.9 + - - -
3805 GLN* 3.5 15.1 + - - +
4135 LYS* 2.7 31.5 + - - +
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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