Contacts of the strand formed by residues 231 - 238 (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 ARG 231 (chain 7).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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707 ASP* 3.5 20.4 - - - +
717 MET* 3.5 24.6 + - + +
827 ARG* 4.5 10.5 - - - +
837 ASN* 3.7 40.2 + - + +
2297 TYR* 3.3 38.7 + - + +
2307 ASN* 1.4 86.8 + - - +
2327 PHE* 1.3 60.9 + - - +
2477 PRO* 5.0 13.3 - - - +
2487 LEU 3.2 8.5 - - - +
2497 SER* 3.7 18.2 - - - +
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Residues in contact with PHE 232 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687 ALA* 4.9 1.8 - - + -
697 ALA 3.5 12.6 - - - +
707 ASP* 3.9 7.2 - - + +
717 MET* 4.2 6.5 - - - -
2157 GLU* 4.5 28.5 - - + -
2187 MET* 3.9 41.3 - - + -
2307 ASN 4.4 7.2 - - - -
2317 ARG* 1.3 76.8 - - - +
2337 GLN* 1.3 72.7 + - - +
2347 ILE* 4.2 13.5 - - + -
2477 PRO* 3.9 3.1 - - - +
2487 LEU* 3.0 73.9 + - + +
2497 SER 4.3 13.0 - - - -
2507 THR* 4.3 9.4 - - + -
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Residues in contact with GLN 233 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687 ALA* 3.6 1.6 - - - -
697 ALA* 2.9 45.4 + - + +
707 ASP 4.5 1.0 + - - -
717 MET* 3.9 26.6 - - + +
857 SER* 3.8 7.9 - - - +
867 ARG* 3.2 39.8 - - - +
877 ILE* 3.6 23.2 - - - +
2327 PHE* 1.3 79.2 - - - +
2347 ILE* 1.4 63.1 + - - +
2447 ILE* 3.9 14.4 - - + +
2457 GLU 3.9 11.4 - - - +
2467 GLY* 4.9 7.2 - - - -
2477 PRO* 5.5 0.4 - - + -
2487 LEU* 5.6 0.4 - - - -
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Residues in contact with ILE 234 (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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667 VAL* 3.8 24.9 - - + -
677 ILE 3.3 12.8 - - - +
687 ALA* 4.0 13.5 - - + -
2117 ARG* 4.4 23.3 - - + +
2147 VAL* 4.9 4.0 - - + -
2157 GLU* 5.8 2.7 - - + +
2327 PHE* 4.2 8.1 - - + -
2337 GLN* 1.4 76.5 - - - +
2357 ALA* 1.4 59.1 + - - +
2367 THR* 4.8 3.1 - - - +
2447 ILE* 3.9 1.6 - - - +
2457 GLU* 2.8 74.0 + - + +
2487 LEU* 3.8 16.8 - - + +
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Residues in contact with ALA 235 (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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667 VAL* 3.7 0.9 - - - +
677 ILE* 2.8 43.2 + - + +
877 ILE* 5.3 4.0 - - + -
957 MET* 4.9 22.9 - - + -
2347 ILE* 1.4 72.6 - - - +
2367 THR* 1.3 62.9 + - - +
2377 VAL* 5.7 1.6 - - + -
2427 VAL* 6.0 3.1 - - + -
2437 GLU 3.4 12.1 - - - +
2447 ILE* 4.2 15.9 - - + -
2457 GLU* 5.7 0.4 - - - -
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Residues in contact with THR 236 (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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617 PHE* 4.0 22.0 - - + -
657 VAL 3.6 12.6 - - - +
667 VAL* 3.8 16.7 - - + +
2117 ARG* 5.8 6.5 + - - +
2347 ILE* 4.8 4.5 - - - +
2357 ALA* 1.3 76.1 + - - +
2377 VAL* 1.3 67.4 - - - +
2387 THR* 4.3 3.1 - - - +
2427 VAL* 3.8 1.1 - - - +
2437 GLU* 2.9 51.7 + - - +
2457 GLU* 4.8 9.8 + - - +
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Residues in contact with VAL 237 (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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647 GLY* 3.1 3.3 - - - -
657 VAL* 2.9 46.8 + - + +
677 ILE* 4.7 3.7 - - + +
937 SER* 4.1 24.2 - - - +
947 THR 4.9 0.7 - - - -
957 MET* 3.7 35.4 - - + +
1597 GLY* 4.3 12.3 - - - -
1607 TYR* 4.3 4.5 - - + +
2357 ALA* 4.3 1.3 - - + -
2367 THR* 1.3 75.2 - - - +
2387 THR* 1.3 70.1 + - - +
2417 GLY 4.1 9.4 - - - +
2427 VAL* 3.9 15.5 - - + -
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Residues in contact with THR 238 (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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617 PHE* 5.5 1.9 - - - -
637 GLY* 3.3 16.0 + - - -
647 GLY* 4.1 0.9 - - - -
1607 TYR* 4.1 4.9 - - - +
2367 THR* 3.8 6.9 - - - -
2377 VAL* 1.3 88.1 - - - +
2397 GLU* 1.3 72.9 + - - +
2407 LYS 3.6 17.6 + - - +
2417 GLY 3.5 14.1 + - - +
2437 GLU* 3.3 30.7 + - - +
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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