Contacts of the strand formed by residues 113 - 121 (chain 3) 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 SER 113 (chain 3).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571 PRO* 3.2 21.2 - - - +
1123 GLY* 1.3 74.0 - - - -
1143 LEU* 1.3 60.1 + - - +
1673 VAL* 4.4 0.4 - - - -
1683 VAL 3.4 13.7 - - - -
1693 PRO* 4.0 0.2 - - - -
1703 TRP* 2.9 17.7 + - - +
2173 CYS* 2.9 38.0 + - - +
2193 ASP* 2.9 28.2 + - - +
2203 PHE* 3.4 9.7 - - - -
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Residues in contact with LEU 114 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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873 LEU* 3.6 33.2 - - + -
893 PRO* 4.4 18.8 - - + -
953 LEU* 6.0 0.7 - - + -
1003 LEU* 3.6 26.2 - - + -
1103 TRP* 4.8 6.5 - - + -
1123 GLY 4.1 0.4 + - - +
1133 SER* 1.3 74.6 - - - +
1153 LYS* 1.3 66.1 + - - +
1163 PHE* 4.7 6.7 - - + -
1673 VAL* 3.5 5.0 - - - +
1683 VAL* 2.7 41.5 + - + +
2143 VAL* 4.8 6.5 - - + -
2153 SER 3.6 9.4 - - - +
2163 ALA* 4.3 1.6 - - - -
2173 CYS* 3.9 2.2 - - - -
2203 PHE* 3.4 32.8 - - + -
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Residues in contact with LYS 115 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521 THR* 3.4 13.5 - - - +
531 ASN* 2.9 27.7 + - - +
541 PRO* 4.4 3.5 - - - +
551 LEU* 3.6 35.0 - - + +
483 GLU 4.4 1.2 + - - -
503 ASP* 4.6 0.9 - - - +
1143 LEU* 1.3 80.3 - - - +
1163 PHE* 1.3 65.9 + - - +
1173 THR* 4.1 2.3 + - - +
1653 THR* 3.8 14.4 - - + -
1663 MET 3.4 9.0 - - - +
1673 VAL* 4.2 5.6 - - + -
1683 VAL 4.5 0.2 - - - +
2133 PHE 3.6 0.7 - - - +
2143 VAL* 3.3 6.2 - - - +
2153 SER* 2.9 62.3 + - - +
2163 ALA 3.7 17.5 + - - -
2173 CYS* 3.9 7.4 - - - +
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Residues in contact with PHE 116 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533 ILE* 3.5 33.2 - - + -
553 PHE* 5.0 0.2 - + - -
853 LEU* 4.0 13.7 - - + -
873 LEU* 4.3 7.4 - - + -
953 LEU* 3.9 24.0 - - + -
1143 LEU* 4.7 4.7 - - + -
1153 LYS* 1.3 74.5 - - - +
1173 THR* 1.3 60.6 + - - +
1183 PHE* 4.0 26.8 + + + -
1643 CYS 3.7 1.0 - - - +
1653 THR* 3.3 2.1 - - - -
1663 MET* 2.8 49.5 + - + +
1683 VAL* 3.7 30.7 - - + -
1903 ILE* 3.8 23.3 - - + -
2133 PHE 3.2 5.2 - - - -
2143 VAL* 3.9 17.5 - - + -
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Residues in contact with THR 117 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451 THR* 3.8 4.9 - - + -
471 VAL* 3.8 27.1 - - + -
531 ASN* 4.7 4.9 - - + +
503 ASP* 4.2 19.7 + - - +
1153 LYS* 4.1 2.5 + - - +
1163 PHE* 1.3 73.5 + - - +
1183 PHE* 1.3 64.1 + - - +
1633 SER* 3.8 14.4 - - - -
1643 CYS 3.2 10.3 - - - +
1653 THR* 2.7 26.5 + - - +
2123 GLY* 3.4 1.2 - - - -
2133 PHE* 2.8 45.0 + - - -
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Residues in contact with PHE 118 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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553 PHE* 3.5 37.7 - + - -
703 VAL* 5.9 0.2 - - + -
833 LEU* 4.2 11.0 - - + -
1163 PHE* 4.0 26.7 - + + -
1173 THR* 1.3 75.5 - - - +
1193 LEU* 1.3 59.4 + - - +
1323 VAL* 3.8 36.6 - - + -
1563 TRP* 3.4 27.8 - + + -
1633 SER* 3.1 8.6 - - - -
1643 CYS* 2.9 35.1 + - + +
1663 MET 5.9 0.4 - - - -
1903 ILE* 5.4 3.8 - - + -
1923 VAL* 3.8 18.2 - - + -
2103 ILE* 4.1 17.0 - - + -
2113 LEU 3.3 15.0 - - - +
2123 GLY* 3.8 4.5 - - - -
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Residues in contact with LEU 119 (chain 3).
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* 3.6 27.1 - - + -
481 GLU* 3.5 13.7 - - - +
1972 ILE* 4.1 20.9 - - + -
1992 ASN* 3.7 10.5 - - - +
1173 THR 4.1 0.6 + - - -
1183 PHE* 1.3 72.6 - - - +
1203 PHE* 1.3 60.0 + - - +
1213 CYS* 3.4 22.5 + - - -
1563 TRP* 4.1 2.5 - - - -
1623 SER* 3.4 29.6 - - - +
1633 SER* 3.5 6.3 - - - +
2103 ILE* 3.2 6.1 - - - -
2113 LEU* 2.8 52.9 + - + +
2133 PHE* 4.4 7.4 - - + -
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Residues in contact with PHE 120 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1992 ASN* 3.0 19.8 + - - -
2012 ARG* 3.4 43.3 + - - +
723 LEU* 4.3 4.0 - - + -
1193 LEU* 1.3 71.7 - - - +
1213 CYS* 1.3 59.4 + - - +
1223 GLY* 3.5 14.6 - - - -
1263 ALA* 3.8 20.6 - - + -
1563 TRP* 3.7 12.8 - - + -
1583 ILE* 3.6 38.4 - - + -
1623 SER* 3.2 20.1 + - - +
1983 ILE* 3.9 14.4 - - + -
2083 MET* 3.7 31.9 - - + -
2103 ILE* 3.7 18.8 - - + -
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Residues in contact with CYS 121 (chain 3).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1192 GLN* 3.5 16.6 - - - +
1202 GLY* 3.9 6.3 + - - -
1212 ALA* 3.9 12.3 - - + -
1992 ASN* 3.6 17.3 - - - +
2352 ALA* 3.8 19.4 - - + +
1193 LEU* 3.7 33.7 - - - -
1203 PHE* 1.3 75.1 - - - +
1223 GLY* 1.3 64.3 + - - +
2083 MET* 4.4 2.4 - - - +
2093 ASP* 2.8 22.6 + - + +
2113 LEU* 3.9 18.2 - - - -
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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