Contacts of the helix formed by residues 391 - 399 (chain J) in PDB entry 6LTJ
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 PHE 391 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22J THR* 4.8 1.3 - - - -
24J ARG* 4.0 16.4 - - - +
32J CYS* 4.1 6.7 - - - -
33J PRO* 3.6 34.8 - - + -
36J ASP* 3.2 35.7 - - + -
387J VAL* 4.9 6.5 - - + -
388J GLU* 4.1 22.1 - - + -
390J ARG* 1.3 97.9 - - + +
392J SER* 1.3 57.9 + - - +
393J SER 3.3 1.6 - - - -
394J TRP* 2.9 25.0 + - + +
395J ILE* 3.0 14.5 + - + +
173K HIS* 3.4 50.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 392 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158J THR* 2.3 32.1 + - - -
161J ALA* 3.3 12.3 - - - +
162J ASN* 5.6 5.4 - - - -
351J ALA* 4.6 6.4 - - - +
383J ASN* 4.6 4.0 - - - -
388J GLU 3.4 20.7 + - - -
389J ARG* 4.0 17.1 + - - +
390J ARG 3.1 3.3 + - - -
391J PHE* 1.3 77.1 - - - +
393J SER* 1.3 64.4 + - - +
395J ILE* 3.0 25.1 + - - +
396J GLY 3.2 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 393 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17J ASP* 4.7 9.3 + - - +
24J ARG* 5.0 12.8 - - - -
123J SER* 5.3 0.5 - - - -
154J THR* 3.4 35.2 - - - +
157J LEU* 3.2 24.7 - - - +
158J THR* 3.7 20.4 - - - +
390J ARG 4.5 1.7 + - - -
391J PHE 3.3 0.2 - - - -
392J SER* 1.3 81.2 + - - +
394J TRP* 1.3 62.9 + - - +
396J GLY 3.0 10.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 394 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J VAL* 2.8 42.6 + - + +
17J ASP* 4.2 12.2 + - + +
24J ARG* 3.1 39.3 + - + +
25J ALA 4.0 0.2 - - - -
26J GLY* 3.5 21.3 - - - +
27J TYR 3.3 28.5 - - - -
30J GLU* 3.9 11.9 - - + -
32J CYS 3.9 2.9 - - - -
33J PRO* 3.5 45.3 - - + -
157J LEU* 5.2 1.6 - - - -
391J PHE* 2.9 16.6 + - - +
393J SER* 1.3 78.5 + - - +
395J ILE* 1.3 75.8 + - + +
397J GLY* 3.0 12.9 + - - +
398J SER* 3.1 26.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 395 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487I LYS* 4.9 18.6 - - + -
30J GLU 4.6 2.2 - - - +
31J ASP 3.5 26.2 - - - +
32J CYS* 4.1 5.6 - - + -
33J PRO* 4.2 3.1 - - + -
161J ALA* 3.8 18.6 - - + +
388J GLU* 5.3 10.1 - - + +
391J PHE* 3.0 21.4 + - + +
392J SER* 3.0 17.4 + - - +
394J TRP* 1.3 97.0 - - + +
396J GLY* 1.3 62.8 + - - +
398J SER* 3.0 6.2 + - - -
399J ILE* 2.9 23.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 396 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157J LEU* 3.2 32.5 - - - -
161J ALA* 3.4 3.5 - - - +
392J SER 3.2 6.1 + - - -
393J SER 3.0 7.6 + - - -
395J ILE* 1.3 75.0 - - - +
397J GLY* 1.3 50.7 + - - +
399J ILE* 3.0 12.8 + - - -
400J LEU* 2.7 40.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 397 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J VAL* 3.6 21.7 - - - +
121J LEU* 3.2 22.6 - - - +
157J LEU* 3.6 14.8 - - - +
393J SER 3.4 6.5 + - - -
394J TRP 3.0 8.8 + - - -
396J GLY* 1.3 75.7 - - - +
398J SER* 1.3 60.9 + - - +
400J LEU 3.0 9.0 + - - -
401J ALA* 3.2 9.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 398 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487I LYS* 5.4 1.3 - - - -
15J VAL* 3.7 10.2 - - - +
27J TYR 3.5 2.6 + - - -
28J ALA* 3.2 4.4 - - - +
29J GLY* 2.5 39.8 + - - +
30J GLU 2.8 18.8 + - - -
394J TRP* 3.1 30.1 + - - -
395J ILE* 3.0 10.1 + - - -
397J GLY* 1.3 73.9 - - - +
399J ILE* 1.3 58.5 + - - +
401J ALA* 3.0 18.0 + - - +
402J SER* 3.8 5.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 399 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480I LEU* 4.8 1.1 - - - +
483I ALA* 3.0 57.4 - - + +
484I LYS* 4.5 2.5 - - + +
486I PHE* 4.0 14.1 - - + -
487I LYS* 3.5 39.9 - - + +
29J GLY* 5.7 0.7 - - - -
160J PHE* 4.8 7.0 - - + +
161J ALA* 4.7 12.1 - - - +
395J ILE* 2.9 16.4 + - + +
396J GLY* 3.0 17.9 + - - +
398J SER* 1.3 75.5 - - - +
400J LEU* 1.3 68.8 + - + +
401J ALA 3.5 0.2 - - - -
402J SER* 4.6 7.0 - - - +
403J LEU* 4.2 5.0 - - - +
----------------------------------------------------------
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