Contacts of the strand formed by residues 1079 - 1084 (chain B) in PDB entry 1Q6P
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 ARG1079 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1073B LYS* 4.7 0.7 - - - +
1074B MET* 2.9 32.4 + - + +
1077B ALA* 3.4 3.1 - - + -
1078B GLN* 1.3 80.6 + - - +
1080B SER* 1.3 70.9 + - - +
1081B TYR* 3.7 24.5 - - + +
1199B ARG* 3.7 8.3 - - - +
1204B LEU* 3.6 51.5 + - - +
1206B PRO* 5.9 3.0 - - - +
1229B ASP* 3.0 38.0 + - - -
1233B LEU* 3.5 43.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER1080 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1071B LEU* 4.1 9.0 - - - +
1072B ILE 3.2 9.0 - - - -
1073B LYS* 3.6 28.1 - - - +
1079B ARG* 1.3 81.1 - - - +
1081B TYR* 1.3 67.8 + - - +
1204B LEU* 5.9 0.2 - - - +
1210B PRO* 3.6 28.4 - - - +
1211B VAL* 4.2 4.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR1081 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1070B SER 3.7 0.2 - - - +
1071B LEU* 3.5 4.7 - - - +
1072B ILE* 2.8 51.8 + - + +
1074B MET* 4.3 10.5 - - + -
1079B ARG* 3.7 23.5 + - + +
1080B SER* 1.3 76.1 - - - +
1082B ILE* 1.3 63.3 + - - +
1083B LEU* 3.7 17.3 - - + -
1204B LEU* 5.0 3.1 - - + -
1210B PRO* 4.1 1.1 - - - -
1211B VAL* 3.7 28.0 - - + +
1213B VAL* 4.6 1.8 - - + -
1225B PHE* 5.2 4.3 - + - -
1226B CYS* 3.6 34.1 - - + -
1229B ASP* 2.7 31.3 + - + -
1230B THR* 2.7 36.3 + - - -
1233B LEU* 4.4 0.2 - - - +
1253B MET* 5.4 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE1082 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1057B ILE* 3.8 34.5 - - + -
1069B ALA* 4.0 5.8 - - + -
1070B SER 3.2 7.9 - - - +
1071B LEU* 4.1 3.4 - - + -
1081B TYR* 1.3 75.3 - - - +
1083B LEU* 1.3 64.7 + - - +
1084B THR 4.0 0.2 + - - -
1098B MET* 3.9 27.6 - - + -
1102B GLN* 3.8 23.6 - - + +
1104B SER* 4.5 3.8 - - - +
1210B PRO* 3.5 34.5 - - + +
1211B VAL 2.9 12.3 + - - +
1212B VAL* 3.6 11.1 - - + +
1213B VAL* 2.7 29.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU1083 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1069B ALA* 3.2 2.5 - - - -
1070B SER 2.8 32.0 + - - -
1072B ILE* 3.9 21.3 - - + -
1081B TYR* 3.7 21.8 - - + -
1082B ILE* 1.3 80.2 - - - +
1084B THR* 1.3 61.0 + - - +
1213B VAL* 3.3 4.9 - - + +
1218B GLY 3.9 9.4 - - - +
1222B SER* 4.0 30.1 - - - +
1223B GLY* 4.3 2.2 - - - +
1226B CYS* 3.9 13.2 - - + -
1253B MET* 6.3 0.4 - - - -
1257B ARG* 3.7 22.6 + - - -
1260B LEU* 3.7 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR1084 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1067B ILE* 4.5 6.4 - - - +
1068B ASN 2.5 23.6 + - - -
1069B ALA* 3.4 14.0 - - - +
1082B ILE* 4.0 0.4 + - - -
1083B LEU* 1.3 75.9 - - - +
1085B GLN* 1.3 74.3 + - - +
1095B PHE* 3.9 25.0 - - + -
1098B MET* 4.1 6.6 - - + +
1212B VAL* 4.0 10.8 - - + -
1213B VAL 3.0 7.3 + - - -
1214B HIS* 3.1 30.8 - - + +
1218B GLY* 3.2 18.6 - - - -
1257B ARG* 4.3 2.7 - - - +
----------------------------------------------------------
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