Contacts of the strand formed by residues 962 - 966 (chain C) in PDB entry 5D6Y
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 VAL 962 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
948C SER* 4.5 2.8 + - - -
949C GLN* 5.0 1.0 - - - +
960C GLY 3.7 1.0 + - - +
961C GLU* 1.3 80.2 - - - +
963C VAL* 1.3 71.6 + - - +
964C GLN* 5.9 2.9 - - + +
975C ALA 3.5 10.5 - - - +
976C LYS* 4.0 25.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 963 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930C VAL* 4.5 4.7 - - + -
946C ILE* 4.1 17.5 - - + -
948C SER* 3.5 13.5 - - - +
949C GLN* 4.2 4.7 - - - +
957C PRO* 3.7 34.1 - - + -
961C GLU* 3.7 8.7 - - + +
962C VAL* 1.3 84.1 - - - +
964C GLN* 1.3 65.1 + - - +
965C VAL* 4.0 20.2 - - + -
974C GLY* 3.7 2.8 - - - -
975C ALA* 2.9 47.2 + - + +
977C PHE* 4.2 10.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 964 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
921B ARG* 4.2 11.1 + - - +
987B GLN* 3.1 30.4 + - - +
995B GLN* 4.9 10.2 + - - +
946C ILE* 3.8 6.2 - - - +
947C VAL* 3.2 26.3 + - + -
948C SER* 3.1 25.6 + - - -
962C VAL* 5.9 3.3 - - + +
963C VAL* 1.3 76.8 - - - +
965C VAL* 1.3 62.2 + - - +
972C VAL* 3.7 17.3 - - + -
973C TYR 3.5 5.2 - - - +
974C GLY* 5.3 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 965 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
930C VAL* 4.3 6.3 - - + -
932C PHE* 3.8 31.0 - - + -
941C LEU* 3.8 25.1 - - + -
945C ASP 3.3 4.9 - - - +
946C ILE* 4.3 10.8 - - + -
963C VAL* 4.0 11.0 - - + -
964C GLN* 1.3 78.5 - - - +
966C ARG* 1.3 73.4 + - - +
967C TRP* 3.4 4.3 + - + +
972C VAL* 3.3 3.3 - - - -
973C TYR* 2.7 37.5 + - - +
975C ALA* 4.0 19.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 966 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
925B GLU* 2.4 44.8 + - - -
927B PHE* 4.2 9.7 - - - -
942B TYR* 3.0 11.6 + - - -
985B MET* 4.8 3.2 - - - +
997B VAL* 4.0 27.2 + - + +
944C GLU 3.6 10.8 + - - -
945C ASP* 2.3 63.9 + - - +
947C VAL* 3.9 25.1 - - + +
965C VAL* 1.3 73.3 - - - +
967C TRP* 1.3 74.9 + - - +
970C GLY* 4.1 19.1 - - - +
971C GLN 3.6 3.8 - - - -
972C VAL* 4.2 3.8 - - - +
19b GLN* 3.9 20.0 + - - +
----------------------------------------------------------
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