Contacts of the helix formed by residues 345 - 350 (chain C) in PDB entry 2XH2
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 LYS 345 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C GLU* 4.9 0.4 + - - -
320C ASP* 2.9 25.2 + - - +
325C THR* 2.9 21.9 + - - -
343C LEU* 3.5 22.6 + - + +
344C LEU* 1.3 74.1 - - - +
346C VAL* 1.3 67.3 + - - +
347C ASN 3.1 0.9 - - - -
348C GLN* 2.9 43.1 + - + +
372C SER* 3.9 20.9 - - - +
373C HIS 3.9 2.0 - - - +
374C ARG* 3.6 33.6 - - - +
1440C 2PG 2.8 40.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 346 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PRO* 5.2 9.6 - - + -
111C LEU* 4.0 27.7 - - + +
115C LEU* 4.7 13.2 - - + -
344C LEU* 3.9 6.7 + - + +
345C LYS* 1.3 71.4 - - - +
347C ASN* 1.3 60.2 + - + +
348C GLN 3.4 0.5 + - - -
349C ILE* 3.4 5.5 + - - +
350C GLY* 2.9 25.6 + - - -
351C THR 5.3 0.4 - - - +
352C LEU* 5.0 2.7 - - + -
355C SER* 3.4 27.1 + - - +
372C SER 5.2 1.4 + - - +
382C PHE* 4.7 10.3 - - + -
383C ILE* 4.9 15.0 - - + +
386C LEU* 3.8 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 347 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C VAL* 4.5 5.4 - - + +
35C PRO* 3.4 34.8 + - + +
36C SER* 4.4 4.9 - - - +
37C GLY 4.8 0.8 - - - +
44C GLU* 4.7 2.8 + - - +
45C ALA 4.4 10.0 - - - +
47C GLU* 4.5 11.9 + - - +
107C ALA* 4.5 11.1 - - + +
108C ASN* 6.2 0.6 - - - +
111C LEU* 3.5 23.3 - - + -
345C LYS* 3.0 1.9 + - - +
346C VAL* 1.3 76.9 - - - +
348C GLN* 1.3 63.1 + - - +
349C ILE 3.2 1.8 - - - -
350C GLY* 4.2 4.6 + - - +
374C ARG* 2.8 45.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 348 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C HIS 4.8 0.7 - - - +
44C GLU* 3.1 43.2 + - + -
45C ALA 2.8 27.2 + - - -
320C ASP* 3.0 26.7 + - - +
321C ALA* 4.8 1.8 - - - +
324C VAL* 3.3 40.9 - - - +
325C THR* 2.8 22.6 + - - +
343C LEU 4.1 3.3 - - - +
345C LYS* 2.9 29.9 + - + +
347C ASN* 1.3 78.6 + - - +
349C ILE* 1.3 58.7 + - - +
374C ARG* 3.5 9.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 349 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA* 3.7 9.6 - - + +
100C ALA 5.8 2.7 - - - +
102C LYS* 2.8 31.9 + - - +
325C THR* 3.3 29.8 - - + +
326C ASN* 3.8 35.4 - - + +
327C PRO* 4.7 3.4 - - + -
346C VAL 3.7 2.2 - - - +
347C ASN 3.2 0.2 - - - -
348C GLN* 1.3 83.3 - - - +
350C GLY* 1.3 59.9 + - - +
351C THR 3.6 7.2 - - - +
354C GLU* 3.7 31.0 - - + +
355C SER* 3.4 30.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 350 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102C LYS* 3.9 11.2 - - - -
107C ALA* 4.2 13.5 - - - -
110C ILE* 3.4 7.4 - - - +
111C LEU* 3.2 35.7 + - - -
346C VAL 2.9 11.9 + - - -
347C ASN* 4.2 3.0 - - - -
348C GLN 3.9 0.2 - - - -
349C ILE* 1.3 77.2 - - - +
351C THR* 1.3 67.8 + - - +
----------------------------------------------------------
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