Contacts of the strand formed by residues 309 - 316 (chain B) in PDB entry 1MWT
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 ILE 309 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG* 4.3 17.0 - - - +
300B THR* 4.0 13.9 - - + -
301B ILE 3.8 4.5 - - - +
302B VAL* 4.7 2.0 - - + +
303B ASP* 5.1 0.2 - - - -
307B ASN 4.6 5.4 - - - +
308B THR* 1.3 72.6 - - - +
310B ALA* 1.3 60.4 + - - +
311B HIS* 3.4 31.0 - - - +
312B THR* 3.7 12.1 - - - +
706B CL 4.1 26.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A THR* 4.8 15.8 + - - +
140B GLN* 3.7 27.1 - - - +
301B ILE* 2.9 13.0 + - + +
303B ASP* 4.0 13.0 - - - +
308B THR 3.3 3.2 + - - -
309B ILE* 1.3 74.7 - - - +
311B HIS* 1.3 78.1 + - + +
707B CL 3.8 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 311 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ASP* 3.4 26.7 + - - -
210A THR* 4.6 3.4 - - - -
211A PHE 5.8 0.6 + - - -
110B ARG* 3.3 31.3 + - - +
135B GLY* 3.3 18.9 + - - -
300B THR* 3.2 7.6 - - - -
301B ILE* 2.9 48.1 + - + -
309B ILE* 3.4 4.6 - - - +
310B ALA* 1.3 97.6 + - + +
312B THR* 1.3 62.2 + - - +
313B LEU* 3.8 7.4 - - + -
702B CD 2.2 31.1 - - - -
707B CL 3.6 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 312 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B ARG* 5.8 2.6 + - - -
298B ARG* 4.3 2.4 - - + -
300B THR* 3.8 16.4 - - + +
309B ILE* 3.7 15.8 - - - +
311B HIS* 1.3 74.8 - - - +
313B LEU* 1.3 64.4 + - - +
314B ILE 4.2 7.0 - - - +
315B GLU* 3.9 34.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 313 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 5.6 0.2 - - + -
107B ASN 4.6 5.0 - - - +
108B ILE* 3.8 39.1 - - + +
110B ARG* 3.8 29.8 - - - +
133B ILE* 3.9 17.5 - - + -
134B PRO 4.3 1.8 - - - +
142B ILE* 4.7 3.8 - - + -
299B VAL* 3.0 26.9 + - + +
300B THR* 4.6 1.1 - - - -
301B ILE* 3.8 39.3 - - + -
311B HIS* 4.4 4.9 - - + -
312B THR* 1.3 75.8 - - - +
314B ILE* 1.3 67.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 314 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B LEU* 6.0 0.7 - - + -
103B THR* 3.7 13.9 - - + +
105B TYR* 3.2 26.2 - - + +
106B GLY* 3.6 31.9 - - - -
107B ASN 4.0 9.0 - - - +
108B ILE* 3.8 24.7 - - + -
297B TYR* 4.1 9.9 - - + +
298B ARG* 3.5 5.2 - - - +
299B VAL* 2.9 41.0 + - + +
312B THR* 4.2 1.9 - - - +
313B LEU* 1.3 86.5 - - + +
315B GLU* 1.3 67.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 315 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 4.7 7.6 - - + -
297B TYR 3.8 8.7 - - - +
298B ARG* 3.5 25.0 + - + +
312B THR* 3.9 16.1 + - + +
314B ILE* 1.3 84.3 - - - +
316B LYS* 1.3 67.6 + - - +
317B LYS* 4.0 29.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 316 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B LEU* 3.8 2.3 - - - +
273B LYS* 4.1 13.9 - - - +
294B GLU* 3.2 18.2 + - - +
295B ASP 4.7 6.6 + - - +
296B GLY* 3.2 5.7 - - - -
297B TYR* 3.0 72.8 + - + +
315B GLU* 1.3 73.8 - - - +
317B LYS* 1.3 72.7 + - - +
318B LYS 3.6 0.2 + - - -
319B LYS* 3.6 22.9 - - - +
----------------------------------------------------------
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