Contacts of the strand formed by residues 10 - 14 (chain D) in PDB entry 1MWA
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 ASN 10 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40C ARG* 5.2 0.8 - - - +
8D PRO* 2.7 13.8 + - - +
9D ARG* 1.3 92.8 + - - +
11D LYS* 1.3 65.2 + - - +
113D ARG* 4.3 11.2 - - - +
156D HIS* 4.5 13.2 - - + -
217D HIS* 3.0 62.1 + - + +
218D GLY 4.9 5.5 - - - +
234D THR* 6.1 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 3.7 22.0 - - + -
10D ASN* 1.3 77.5 - - - +
12D VAL* 1.3 87.1 + - - +
13D ALA* 3.7 14.5 + - + +
14D VAL* 6.3 0.9 - - - -
19D VAL* 4.7 19.1 - - + -
21D LEU* 6.0 0.4 - - + -
113D ARG* 3.8 8.5 + - - +
114D LEU* 4.0 8.4 - - + +
115D SER* 3.2 23.8 + - - -
156D HIS* 4.5 4.9 + - - -
218D GLY 5.6 4.9 + - - +
219D LEU* 4.2 20.0 - - - +
220D SER* 4.8 16.6 + - - +
223D ASP* 5.1 4.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LYS* 1.3 91.9 + - - +
13D ALA* 1.3 74.8 + - - +
14D VAL* 5.1 0.7 - - - +
115D SER* 3.3 29.8 - - - +
118D ASP 5.8 1.3 - - - +
119D LEU* 4.1 27.0 - - + +
122D VAL* 4.7 20.9 - - + -
153D PHE* 5.8 4.7 - - + -
154D PRO* 5.5 3.6 - - + -
156D HIS* 4.4 13.9 - - + +
217D HIS 5.2 6.3 - - - +
218D GLY* 6.0 4.7 - - - -
219D LEU* 4.9 8.2 - - + +
316D LEU* 5.7 4.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LYS* 3.6 12.7 + - - +
12D VAL* 1.3 92.2 - - - +
14D VAL* 1.3 68.8 + - - +
17D GLY 4.4 1.8 - - - +
19D VAL* 3.3 33.2 - - + -
82D ALA* 4.9 2.0 - - + -
86D GLN* 5.7 0.2 - - - +
114D LEU* 3.6 21.0 - - + +
115D SER 3.9 5.7 + - - +
116D VAL* 3.6 15.1 - - + -
119D LEU* 4.7 5.5 - - - +
316D LEU 4.7 2.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LYS* 6.3 0.9 - - - -
12D VAL 5.1 0.4 - - - +
13D ALA* 1.3 83.1 - - - +
15D THR* 1.3 68.2 + - - +
16D GLY* 2.9 9.0 + - - +
17D GLY* 3.1 30.6 + - - +
82D ALA* 3.3 19.6 - - - +
116D VAL* 4.0 3.4 - - - +
119D LEU* 5.0 22.4 - - + -
316D LEU 4.1 7.6 - - - +
----------------------------------------------------------
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