Contacts of the helix formed by residues 391 - 395 (chain A) in PDB entry 4YVE
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 391 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 4.1 17.9 - - + +
39A TYR* 4.2 19.3 - - + -
40A ASP* 2.8 27.3 + - - +
109A LYS* 3.2 14.7 + - - +
144A GLN* 4.8 3.9 - - - +
145A ASP 3.0 24.3 - - - +
146A ASP* 2.8 33.5 + - - +
381A PHE* 4.2 16.6 - - - -
390A ASN* 1.4 73.6 - - - +
392A LEU* 1.3 64.8 + - - +
393A PRO 3.6 0.7 - - - -
394A PHE* 3.5 16.1 + - + +
395A VAL* 3.5 14.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 392 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ALA* 5.2 5.4 - - + -
37A LEU* 6.1 0.9 - - + +
40A ASP* 3.8 3.6 + - - +
387A PHE* 4.2 10.8 - - + -
389A GLY* 3.2 29.9 + - - +
391A GLN* 1.3 73.4 - - - +
393A PRO* 1.4 61.5 - - + +
394A PHE 2.8 11.2 + - - -
395A VAL* 3.1 21.9 + - + +
37B LEU* 3.8 25.4 - - + -
41B LEU* 4.2 7.9 - - + -
51B ASN 4.0 8.5 - - - +
52B ILE* 4.1 21.8 - - + -
55B PHE* 3.7 42.4 - - + -
58B ARG* 3.4 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 393 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ILE* 4.0 11.7 - - + -
121A PHE* 4.1 3.7 - - + -
122A TRP* 3.4 23.2 + - - -
389A GLY 3.7 5.4 - - - +
390A ASN 3.3 17.0 - - - +
392A LEU* 1.4 88.1 - - + +
394A PHE* 1.3 71.5 + - + +
395A VAL 3.7 0.4 - - - -
51B ASN* 3.3 30.7 - - + +
54B ASN* 5.9 6.3 - - + +
55B PHE* 6.0 1.8 - - + +
58B ARG* 4.1 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 394 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A LYS* 3.4 39.9 - - + +
112A MET* 4.1 19.7 - - + -
113A ILE* 3.8 28.3 - - + -
121A PHE* 3.8 28.7 - + - -
122A TRP* 4.1 6.5 - - - -
144A GLN* 2.8 45.9 + - - +
149A LEU* 3.9 16.4 - - + -
381A PHE* 5.3 1.8 - + - -
390A ASN 3.3 27.1 - - - -
391A GLN* 4.0 8.5 - - - +
392A LEU 2.8 3.8 + - - -
393A PRO* 1.3 80.5 - - + +
395A VAL* 1.4 60.5 + - - +
396A GLY 3.3 0.5 + - - -
397A PHE* 3.3 8.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 395 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A CYS 3.7 7.4 - - - +
32A ASP* 4.3 4.7 - - - +
33A GLY* 3.6 28.7 - - - +
36A ALA* 3.7 22.9 - - + -
122A TRP* 3.8 2.4 - - - -
144A GLN* 4.7 0.4 - - - +
391A GLN 3.5 12.8 - - - +
392A LEU* 3.1 23.1 + - + +
393A PRO 3.7 0.4 - - - -
394A PHE* 1.4 75.4 - - - +
396A GLY* 1.3 61.8 + - - +
34B LEU* 5.3 2.9 - - + -
55B PHE* 4.0 21.8 - - + -
58B ARG* 3.0 28.8 + - - +
59B TYR* 3.7 14.2 + - + +
----------------------------------------------------------
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