Contacts of the strand formed by residues 64 - 70 (chain 7) in PDB entry 5LN3
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 64 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607 LYS 3.9 0.2 - - - -
617 PHE* 2.8 42.3 + - - +
627 GLU 3.3 0.4 + - - -
637 GLY* 1.4 78.8 - - - +
657 VAL* 1.4 63.6 + - - +
1597 GLY 5.6 0.7 - - - -
1607 TYR* 5.9 0.7 - - - -
1657 SER* 3.3 12.8 + - - -
2377 VAL 3.1 13.7 - - - -
2387 THR 4.5 0.2 - - - -
2397 GLU* 3.7 9.4 + - - -
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Residues in contact with VAL 65 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597 VAL 3.3 16.8 - - - +
607 LYS* 4.0 17.3 - - + +
617 PHE* 3.6 2.7 - - - -
647 GLY* 1.4 77.1 - - - +
667 VAL* 1.3 67.3 + - - +
677 ILE* 4.0 15.7 - - + -
1587 GLY 4.6 0.9 - - - -
1597 GLY 3.9 20.6 - - - +
1657 SER* 4.4 3.1 - - - -
1667 PHE 3.6 22.0 - - - +
1677 LEU* 4.2 7.6 - - + -
2367 THR* 3.6 2.1 - - - +
2377 VAL* 2.9 48.0 + - + +
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Residues in contact with VAL 66 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587 GLY* 3.4 2.4 - - - -
597 VAL* 3.0 47.9 + - + +
617 PHE* 3.7 25.8 - - + -
657 VAL* 1.3 80.9 - - - +
677 ILE* 1.4 69.0 + - - +
2107 ALA* 4.6 9.4 - - + +
2117 ARG* 4.7 9.6 - - + +
2147 VAL* 4.7 12.3 - - + -
2347 ILE* 3.8 29.4 - - + -
2357 ALA 3.7 3.6 - - - +
2367 THR* 3.8 16.6 - - + +
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Residues in contact with ILE 67 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567 VAL* 4.7 11.7 - - + -
577 LEU 3.5 12.3 - - - +
587 GLY* 4.3 3.8 - - - -
657 VAL* 4.0 23.8 - - + +
667 VAL* 1.4 83.5 - - - +
687 ALA* 1.3 72.8 + - - +
697 ALA* 5.5 2.0 - - + -
957 MET* 4.2 41.7 - - + +
977 GLY* 5.1 4.9 - - - +
1567 VAL* 5.4 8.1 - - + -
1587 GLY* 5.3 4.0 - - - -
1677 LEU* 5.1 10.1 - - + -
2147 VAL* 5.4 0.7 - - - -
2347 ILE* 3.3 5.1 - - - +
2357 ALA* 2.8 47.5 + - + +
2377 VAL* 4.7 6.3 - - + -
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Residues in contact with ALA 68 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567 VAL* 3.6 0.7 - - - -
577 LEU* 2.8 38.0 + - + +
677 ILE* 1.3 80.9 - - - +
697 ALA* 1.4 63.9 + - - +
2147 VAL* 3.7 24.2 - - + +
2187 MET* 3.7 20.6 - - + -
2327 PHE* 4.9 2.5 - - + -
2337 GLN 3.6 9.4 - - - +
2347 ILE* 4.0 12.6 - - + -
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Residues in contact with ALA 69 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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557 SER 3.9 11.7 - - - +
567 VAL* 4.0 10.3 - - + -
677 ILE* 5.5 2.5 - - + -
687 ALA* 1.4 76.1 - - - +
707 ASP* 1.4 59.2 + - - +
867 ARG* 3.7 29.4 - - + -
2187 MET* 3.8 7.8 - - - +
2327 PHE* 3.5 0.3 - - - +
2337 GLN* 2.9 44.3 + - + +
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Residues in contact with ASP 70 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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547 THR 2.9 22.3 - - - +
557 SER* 3.2 12.9 + - - +
697 ALA* 1.4 76.6 - - - +
717 MET* 1.4 63.6 + - - +
727 LEU* 3.6 23.4 - - + +
867 ARG* 2.9 38.8 + - - +
2187 MET* 4.3 10.8 - - - +
2217 LEU* 5.7 0.4 - - - +
2287 SER* 4.7 7.9 - - - -
2297 TYR 4.3 16.3 + - - +
2317 ARG 3.5 17.0 - - - +
2327 PHE* 3.9 6.9 - - + +
2337 GLN* 4.5 0.9 + - - -
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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
------------------------------------------------------------
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