Contacts of the strand formed by residues 117 - 127 (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 PHE 117 (chain 2).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1152 SER* 2.9 12.1 + - - +
1162 LYS* 1.3 87.6 - - + +
1182 HIS* 1.3 57.9 + - - +
2392 PHE* 3.4 23.1 - - + -
2402 ALA 3.7 0.2 + - - -
1233 SER* 3.9 7.0 - - - -
1253 MET* 3.6 40.6 - - + -
2013 PRO* 4.3 7.0 - - + -
2023 LEU 4.0 7.4 - - - -
2033 SER* 3.7 19.7 - - - +
2043 THR* 3.2 26.2 - - - +
2053 PRO* 3.4 21.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 118 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1142 ALA* 3.8 25.4 - - + -
1152 SER* 2.8 47.7 + - - +
1162 LYS 4.5 0.2 - - - -
1172 PHE* 1.3 78.6 - - - +
1192 GLN* 1.3 60.4 + - - +
2002 LEU* 4.2 10.4 - - + +
2012 ARG 5.0 1.4 + - - -
2372 LEU* 4.4 9.0 - - + -
2382 ASN 3.3 8.1 - - - +
2392 PHE* 3.3 49.3 - + + +
2452 PRO* 5.3 3.6 - - + +
2462 GLU 5.1 2.4 + - - -
2472 ILE* 4.2 18.1 - - + +
1223 GLY 4.6 0.2 - - - +
1233 SER* 3.2 18.0 - - - -
1243 MET 4.6 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1182 HIS* 1.3 77.0 - - - +
1202 GLY* 1.3 59.4 + - - +
2002 LEU* 3.7 9.9 - - - -
2362 PRO 4.8 2.2 + - - +
2372 LEU* 3.4 6.8 - - - +
2382 ASN* 2.8 60.4 + - + +
1213 CYS 3.5 13.4 + - - +
1223 GLY* 3.5 15.8 - - - -
1233 SER* 3.4 13.7 + - - +
2053 PRO* 3.4 26.5 - - + +
2073 GLU 2.8 24.3 + - - +
2083 MET* 3.7 18.4 - - - +
2093 ASP 5.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 120 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712 TRP* 3.7 14.6 - - - -
1192 GLN* 1.3 78.8 - - - +
1212 ALA* 1.3 60.7 + - - -
1982 ILE 3.7 0.2 - - - +
1992 ASN* 3.5 6.1 + - - +
2002 LEU* 3.0 29.1 + - - +
2352 ALA* 3.4 17.3 - - - -
2362 PRO 3.6 6.7 - - - -
1213 CYS 3.9 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712 TRP* 3.7 2.3 - - - -
1202 GLY* 1.3 76.5 - - - +
1222 LEU* 1.3 57.9 + - - +
1972 ILE* 4.1 15.0 - - + -
1982 ILE 3.2 6.3 - - - +
1992 ASN* 3.9 13.2 - - + +
2332 PRO* 3.5 1.6 - - - +
2342 LEU* 2.7 37.9 + - + -
2352 ALA* 2.9 30.2 + - + +
1213 CYS* 3.9 11.2 - - - -
2113 LEU* 5.0 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 122 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
712 TRP* 3.6 47.6 - - + -
782 TRP* 4.3 6.5 - - + -
1102 VAL* 5.4 0.2 - - + -
1122 CYS* 4.3 13.2 - - + -
1212 ALA* 1.3 72.9 - - - +
1232 GLY* 1.3 61.5 + - - +
1242 VAL* 3.5 4.1 + - + +
1972 ILE* 3.2 7.4 - - - -
1982 ILE* 2.8 57.4 + - + +
2312 ILE* 4.2 21.3 - - + -
2322 LEU 3.5 1.3 - - - -
2332 PRO* 4.2 11.9 - - + -
2492 ILE* 3.6 33.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 123 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1222 LEU* 1.3 71.3 - - - +
1242 VAL* 1.3 59.0 + - - +
1252 PHE* 3.5 21.2 - - - -
1962 GLN 4.0 3.8 - - - -
1972 ILE* 4.6 2.0 - - - -
2302 ALA 3.4 2.1 - - - +
2312 ILE* 3.2 5.9 - - - -
2322 LEU 2.8 37.9 + - - -
2342 LEU* 3.6 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1082 VAL* 5.6 1.1 - - + -
1102 VAL* 3.7 26.5 - - + -
1222 LEU* 4.1 9.2 - - + +
1232 GLY* 1.3 74.6 - - - +
1252 PHE* 1.3 64.0 + - - +
1952 HIS* 3.2 6.3 - - - +
1962 GLN 2.9 37.4 + - - +
1982 ILE* 4.1 14.8 - - + -
2062 ALA* 4.0 24.5 - - + -
2082 LEU* 4.1 15.4 - - + +
2292 ILE* 4.8 7.9 - - + -
2302 ALA 3.6 2.5 - - - -
2312 ILE* 4.3 22.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 125 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1232 GLY* 3.5 27.1 - - - -
1242 VAL* 1.3 74.0 - - - +
1262 ALA* 1.3 60.1 + - - +
1272 VAL* 3.9 16.1 + - + -
1812 LEU* 5.3 1.8 - - + -
1872 LEU* 4.6 6.5 - - + -
1902 ALA* 3.4 50.0 - - + +
1912 PHE* 3.8 36.6 - + - -
1932 PHE* 4.8 1.3 - - + -
1942 PRO 3.8 1.6 - - - +
1952 HIS* 3.7 16.2 - - + -
1962 GLN 5.9 0.2 - - - -
2082 LEU* 4.5 1.6 - - - -
2282 GLY 3.5 1.0 - - - +
2292 ILE* 3.4 6.0 - - - +
2302 ALA* 2.8 51.7 + - + +
2322 LEU* 4.3 18.8 - - + -
2342 LEU* 4.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1252 PHE* 1.3 72.4 - - - +
1272 VAL* 1.3 59.0 + - - +
1932 PHE* 3.4 16.6 - - - +
1942 PRO* 2.9 25.0 + - + +
2082 LEU* 3.6 16.2 - - + +
2102 LEU* 3.5 37.5 - - + -
2272 TRP* 3.5 12.3 - - + -
2282 GLY 3.4 4.7 - - - -
2292 ILE* 4.1 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain 2).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2721 ARG* 4.2 5.6 - - - +
1252 PHE* 4.3 15.9 - - + +
1262 ALA* 1.3 75.8 - - - +
1282 PRO* 1.3 75.8 - - - +
1292 GLU 3.6 0.3 + - - -
1302 MET* 3.7 41.3 + - + -
1812 LEU* 5.3 6.7 - - + -
1832 ASN* 5.5 3.1 - - - +
1932 PHE* 3.7 43.1 - - + -
2272 TRP* 3.5 3.5 - - - -
2282 GLY* 2.8 35.9 + - - +
2302 ALA* 5.0 1.6 - - + -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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