Contacts of the strand formed by residues 27 - 31 (chain D) in PDB entry 6CIM
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 27 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D ASN* 3.3 2.1 - - - +
24D PHE 2.9 37.0 + - - +
25D ASP* 3.1 6.4 + - + +
26D GLY* 1.3 77.9 - - - +
28D VAL* 1.3 61.6 + - - +
29D PHE* 3.7 15.5 - - + -
47D HIS* 2.9 30.3 + - + -
115D LYS* 4.5 10.5 - - - +
118D LYS* 3.6 32.6 + - + +
120D VAL* 3.3 31.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 4.2 15.0 - - + -
22D MET 3.6 6.7 - - - +
23D ASN* 4.2 8.1 - - - +
26D GLY 4.2 6.3 - - - +
27D GLN* 1.3 75.6 - - - +
29D PHE* 1.3 76.0 + - - +
47D HIS* 3.8 8.8 + - - -
48D PHE* 2.9 56.3 + - + +
322D MET* 3.6 39.0 - - + +
324D ASN* 4.6 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 29 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D LEU* 3.1 12.5 - - - +
22D MET* 2.8 49.6 + - + +
24D PHE* 4.1 17.3 - + + -
27D GLN* 3.7 44.9 - - + -
28D VAL* 1.3 72.9 - - - +
30D PHE* 1.3 59.9 + - - +
45D VAL* 4.5 8.1 - - + -
46D PHE 3.1 19.1 - - - +
47D HIS* 3.7 26.7 - - + -
48D PHE* 4.2 1.3 - - - -
60D ALA* 4.7 4.3 - - + -
112D VAL* 5.8 0.2 - - + -
120D VAL* 4.1 16.6 - - + -
122D PHE* 3.4 41.7 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 30 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LEU* 3.9 13.0 - - + -
15D ILE* 3.9 35.2 - - + -
19D PHE* 3.4 42.6 - + + -
20D SER 3.5 2.9 - - - -
21D LEU* 3.6 10.8 - - + -
29D PHE* 1.3 74.1 - - - +
31D PHE* 1.3 64.6 + - - +
32D GLY 4.1 13.0 - - - -
33D GLN* 4.0 24.5 - - + -
44D GLY 4.0 0.2 - - - +
45D VAL* 3.5 6.2 - - - +
46D PHE* 2.9 52.4 + + + +
48D PHE* 3.9 18.8 - + + -
57D LEU* 4.4 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 31 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19D PHE* 3.7 2.8 - - - +
20D SER* 2.9 49.3 + - - +
22D MET* 5.1 15.3 - - + -
30D PHE* 1.3 80.3 - - - +
32D GLY* 1.3 68.1 + - - +
33D GLN 3.8 0.2 - - - -
43D THR 6.0 0.7 - - - -
44D GLY 4.2 8.1 - - - -
45D VAL* 4.2 22.9 - - + -
69D LEU* 3.6 39.9 - - + -
70D PRO 3.7 16.2 - - - -
71D PRO* 4.1 6.1 - - + -
72D LEU* 3.7 30.7 - - + -
75D PRO* 4.7 3.6 - - + -
93D ILE* 4.2 26.0 - - + -
110D MET* 6.4 0.9 - - - -
----------------------------------------------------------
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