Contacts of the strand formed by residues 277 - 282 (chain E) in PDB entry 3HN3
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 GLN 277 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246E TYR* 3.2 21.1 - - - +
247E GLN* 4.4 13.6 - - + +
274E THR 3.6 13.2 - - - +
275E GLY* 3.2 2.4 - - - -
276E THR* 1.3 86.5 + - - +
278E GLY* 1.3 59.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 278 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245E ASN* 3.5 4.6 + - - +
246E TYR* 2.9 47.3 + - - +
277E GLN* 1.3 80.0 - - - +
279E GLN* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 279 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243E LEU* 4.1 33.2 - - + +
244E VAL 3.3 9.9 - - - +
245E ASN* 2.8 32.0 + - - +
246E TYR* 3.8 0.8 + - - -
278E GLY* 1.3 75.6 - - - +
280E LEU* 1.3 76.4 + - - +
281E LYS* 4.2 2.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 280 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242E GLY 3.6 0.9 - - - +
243E LEU* 3.4 5.2 - - - -
244E VAL* 2.8 47.1 + - + +
246E TYR* 3.7 26.5 - - + -
260E VAL* 4.4 4.5 - - + +
261E ARG 4.7 0.2 - - - -
262E LEU* 4.1 23.6 - - + +
271E ALA* 4.0 10.5 - - + +
272E ASN* 3.4 38.4 - - - +
273E GLY* 3.6 5.2 - - - +
279E GLN* 1.3 80.3 - - - +
281E LYS* 1.3 59.8 + - - +
282E VAL* 4.2 1.5 + - + -
303E LEU* 3.7 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 281 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238E GLU* 3.9 21.9 + - - +
241E SER* 4.3 15.5 - - - +
242E GLY 3.4 7.2 - - - +
243E LEU* 4.2 12.3 - - + -
270E VAL 4.2 0.5 - - - +
271E ALA* 3.5 15.5 - - - +
279E GLN* 4.2 2.7 + - - +
280E LEU* 1.3 72.6 - - - +
282E VAL* 1.3 63.9 + - - +
283E PRO* 3.4 13.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 282 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241E SER* 3.3 5.2 - - - -
242E GLY 2.8 36.7 + - - +
244E VAL* 4.4 4.7 - - + -
262E LEU* 3.4 30.1 - - + -
270E VAL* 3.9 24.2 - - + -
271E ALA* 4.5 3.8 - - + -
280E LEU 4.6 1.6 - - - +
281E LYS* 1.3 76.7 - - - +
283E PRO* 1.3 72.8 - - + +
285E VAL* 3.5 12.0 - - + +
301E TYR* 3.6 26.7 - - + +
326E ILE* 4.1 8.1 - - + -
----------------------------------------------------------
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