Contacts of the strand formed by residues 3053 - 3058 (chain C) in PDB entry 1HKN
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 GLU3053 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3048C ALA* 3.1 4.2 - - - -
3049C GLU* 3.0 32.6 + - + +
3050C SER* 3.1 35.1 + - - +
3051C VAL 3.1 7.5 + - - +
3052C GLY* 1.3 77.7 - - - +
3054C VAL* 1.3 62.2 + - - +
3084C LEU* 4.5 8.7 - - + +
3085C PHE 3.5 4.7 - - - +
3086C LEU* 3.7 21.6 - - + +
3100C LYS* 2.6 42.9 + - + +
5050E SER* 4.9 11.8 + - - -
5051E VAL* 5.4 1.6 - - - +
5053E GLU* 5.3 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL3054 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3046C LEU* 4.7 8.5 - - + -
3047C SER 3.3 12.3 - - - +
3048C ALA* 4.3 10.8 - - + +
3052C GLY 4.7 0.9 - - - -
3053C GLU* 1.3 83.3 - - - +
3055C TYR* 1.3 64.7 + - - +
3056C ILE* 4.1 12.7 + - + -
3083C CYS 3.7 1.0 - - - +
3084C LEU* 3.6 8.3 - - - +
3085C PHE* 2.8 46.0 + - + +
3087C GLU* 4.1 28.3 - - + +
3097C TYR* 3.9 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR3055 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3045C GLN 3.6 1.4 - - - +
3046C LEU* 3.3 8.0 - - - +
3047C SER* 2.9 44.5 + - - +
3049C GLU* 3.1 37.0 + - + -
3054C VAL* 1.3 74.0 - - - +
3056C ILE* 1.3 60.9 + - - +
3057C LYS* 3.9 1.8 - - + +
3064C TYR* 3.7 29.6 - + + -
3079C PRO* 4.1 21.0 - - + +
3080C ASN* 4.2 7.7 + - - -
3083C CYS* 3.7 29.4 - - + -
3084C LEU* 3.6 28.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE3056 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3014C LEU* 4.3 13.9 - - + -
3025C ILE* 4.2 1.7 - - + +
3044C LEU* 3.8 34.1 - - + -
3045C GLN 3.9 2.5 - - - -
3046C LEU* 4.1 10.5 - - + -
3054C VAL* 4.1 11.8 + - + -
3055C TYR* 1.3 77.0 - - - +
3057C LYS* 1.3 59.5 + - - +
3063C GLN 4.1 0.2 - - - +
3064C TYR* 3.5 2.4 - - - -
3065C LEU* 2.8 66.9 + - + +
3083C CYS 4.5 4.9 + - - -
3085C PHE* 4.4 11.7 - - + -
3097C TYR* 3.8 34.5 - - + -
3109C VAL* 6.0 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS3057 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3044C LEU* 3.3 5.4 - - - -
3045C GLN* 2.7 65.0 + - - +
3047C SER* 6.1 0.2 - - - +
3055C TYR* 5.2 1.3 - - + -
3056C ILE* 1.3 76.9 - - - +
3058C SER* 1.3 75.2 + - - +
3059C THR* 5.0 3.4 - - - +
3062C GLY* 3.3 34.3 - - - +
3063C GLN 3.4 6.3 - - - +
3064C TYR* 4.0 31.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER3058 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3025C ILE* 4.4 15.3 + - - +
3041C HIS* 4.6 8.8 - - - -
3043C GLN 3.6 8.7 + - - -
3044C LEU* 3.8 11.4 - - - +
3057C LYS* 1.3 73.5 - - - +
3059C THR* 1.3 58.3 + - - +
3060C GLU* 3.2 10.7 + - - +
3061C THR* 3.0 37.3 + - - +
3062C GLY* 2.8 28.9 + - - -
3063C GLN 2.9 14.1 + - - -
----------------------------------------------------------
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