Contacts of the strand formed by residues 194 - 200 (chain 2) in PDB entry 1AR9
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 PRO 194 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322 VAL* 4.3 11.0 - - + -
342 ALA* 3.6 38.4 - - + -
352 TYR* 3.7 34.1 - - + +
1252 PHE* 3.8 0.2 - - - -
1262 ALA* 2.9 48.1 + - + +
1922 VAL 4.2 0.4 - - - +
1932 PHE* 1.3 81.0 - - + +
1952 HIS* 1.3 59.7 + - - +
2082 LEU* 3.7 7.0 - - + +
2102 LEU* 5.1 0.4 - - + -
2272 TRP* 4.2 6.3 - - + -
564 PRO* 5.5 7.9 - - + -
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Residues in contact with HIS 195 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471 VAL 4.8 2.8 + - - -
501 GLY* 3.1 51.8 + - - +
322 VAL* 3.6 10.4 - - - +
1242 VAL 3.2 14.6 - - - +
1252 PHE* 3.7 15.0 - - + -
1912 PHE* 3.0 56.5 + + + -
1932 PHE 2.8 20.3 + - - +
1942 PRO* 1.3 74.9 - - - +
1962 GLN* 1.3 76.7 + - - +
1972 ILE* 4.7 4.2 - - + +
2082 LEU* 4.3 5.8 - - - +
493 ILE* 5.5 2.7 - - + -
503 ASP 5.4 0.7 - - - -
534 PHE 5.8 2.0 - - - -
564 PRO* 5.9 2.0 - - + +
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Residues in contact with GLN 196 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481 GLU 3.3 8.1 - - - +
491 THR* 2.9 19.8 + - - +
292 ALA* 2.8 31.7 + - - +
302 ASN 3.4 17.2 + - - +
312 SER* 3.7 4.6 - - - +
322 VAL* 3.7 7.5 - - + +
1232 GLY* 4.0 0.2 - - - -
1242 VAL* 2.9 32.8 + - - +
1952 HIS* 1.3 84.7 - - - +
1972 ILE* 1.3 68.2 + - - +
1982 ILE 4.2 0.2 - - - -
2052 CYS 4.2 3.3 - - - +
2062 ALA* 3.4 20.8 - - + -
2072 THR 2.9 32.5 + - - +
2082 LEU* 4.3 8.3 - - + +
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Residues in contact with ILE 197 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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471 VAL* 4.0 32.8 - - + +
481 GLU* 3.0 27.1 + - + +
1212 ALA* 4.1 17.9 - - + -
1222 LEU 3.2 12.1 - - - +
1232 GLY* 4.6 1.1 - - - -
1912 PHE* 3.8 27.6 - - + -
1952 HIS* 4.7 2.5 - - + -
1962 GLN* 1.3 78.6 - - - +
1982 ILE* 1.3 69.3 + - - +
1992 ASN* 4.0 7.6 - - + +
2032 ASN* 2.9 19.7 + - - +
2342 LEU* 4.0 17.3 - - + -
1193 LEU* 4.1 10.5 - - + -
2133 PHE* 4.3 5.6 - - + -
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Residues in contact with ILE 198 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1102 VAL* 3.7 32.3 - - + +
1122 CYS* 4.1 19.3 - - + +
1202 GLY 3.7 1.7 - - - +
1212 ALA* 3.2 2.3 - - - -
1222 LEU* 2.8 52.4 + - + +
1242 VAL* 4.1 8.1 - - + -
1962 GLN 4.2 0.2 - - - -
1972 ILE* 1.3 72.8 - - - +
1992 ASN* 1.3 56.3 + - - +
2002 LEU* 3.8 9.2 + - + +
2032 ASN* 3.4 23.1 - - - +
2042 ASN 4.1 3.6 - - - -
2052 CYS* 3.7 24.9 - - - +
2062 ALA* 3.7 24.9 - - + +
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Residues in contact with ASN 199 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481 GLU* 3.1 33.8 + - + +
1202 GLY 3.5 12.3 + - - +
1212 ALA* 3.9 7.0 - - + +
1972 ILE* 3.4 4.4 + - + -
1982 ILE* 1.3 72.2 - - - +
2002 LEU* 1.3 55.5 + - - +
2012 ARG* 3.6 15.4 + - - +
2022 THR* 2.7 27.4 + - - -
2032 ASN* 3.0 16.8 + - - -
1193 LEU* 3.7 9.4 - - + +
1203 PHE 3.0 25.3 + - - -
1213 CYS* 3.6 27.1 - - - +
1223 GLY 4.7 0.3 - - - +
1623 SER* 4.5 0.6 - - - -
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Residues in contact with LEU 200 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272 GLU* 5.0 4.7 - - - +
712 TRP* 4.0 12.6 - - + -
1122 CYS* 3.9 23.1 - - - +
1132 ASN* 5.1 0.2 - - - -
1142 ALA* 4.0 19.9 - - + +
1152 SER 5.2 6.7 + - - +
1182 HIS* 4.2 5.2 - - + +
1192 GLN* 3.7 33.2 - - - +
1202 GLY 3.0 22.6 + - - +
1982 ILE* 3.8 8.7 + - + +
1992 ASN* 1.3 71.1 + - - +
2012 ARG* 1.3 60.9 + - - +
2022 THR 3.3 0.9 + - - -
2032 ASN 3.9 11.4 + - - +
2372 LEU* 4.0 8.7 - - + -
2472 ILE* 3.8 31.4 - - + -
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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