Contacts of the strand formed by residues 207 - 213 (chain H) in PDB entry 4D1Q
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 LEU 207 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162H ILE* 4.5 10.3 - - + -
166H ILE* 4.3 16.6 - - + -
195H THR* 2.9 23.1 - - - +
196H LEU* 2.9 37.8 + - + +
198H TYR* 5.0 5.4 - - + -
205H ARG* 4.4 7.0 - - + -
206H ASP* 1.3 76.2 + - - +
208H ILE* 1.3 64.6 + - - +
209H LEU* 3.4 27.9 + - + -
599H PHE* 6.1 2.5 - - + -
602H SER* 3.4 8.5 - - - +
603H PHE* 5.0 1.6 - - - +
606H ASN* 3.0 44.4 - - + +
607H PHE* 4.4 16.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 208 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194H VAL 3.9 5.2 - - - +
195H THR* 4.0 6.1 - - + -
206H ASP* 4.8 5.4 - - - +
207H LEU* 1.3 74.0 - - - +
209H LEU* 1.3 64.3 + - - +
210H GLY* 4.0 18.2 - - - +
574H THR* 3.1 40.4 - - + +
577H LEU* 5.2 11.0 - - + -
598H LEU* 4.5 28.3 - - + +
599H PHE* 3.9 16.0 - - - +
602H SER* 3.0 49.2 + - - +
605H LYS* 5.1 11.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 209 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159H LYS* 3.8 7.1 + - - -
166H ILE* 4.3 6.7 - - + -
194H VAL* 2.7 25.1 + - + +
196H LEU* 3.7 27.1 - - + +
207H LEU* 3.4 36.5 + - + -
208H ILE* 1.3 75.1 - - - +
210H GLY* 1.3 59.0 + - - +
231H ILE* 4.3 5.6 - - + +
232H PHE* 3.6 36.6 - - + -
235H PHE* 3.7 39.9 - - + -
599H PHE* 3.4 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 210 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159H LYS* 5.0 0.4 - - - -
192H LEU 3.7 1.4 - - - +
193H GLY* 3.7 1.2 - - - -
194H VAL* 3.1 27.3 + - - +
208H ILE* 3.4 11.2 - - - +
209H LEU* 1.3 84.2 - - - +
211H LEU* 1.3 61.5 - - - +
212H LYS 4.0 1.8 - - - -
231H ILE* 4.3 13.3 - - - +
595H ASP* 3.3 15.5 - - - -
598H LEU* 5.8 0.7 - - - -
599H PHE* 5.5 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 211 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182H TRP* 4.6 4.0 - - + -
191H PHE* 3.4 47.3 - - + -
192H LEU 3.4 15.9 - - - +
193H GLY* 3.8 9.4 - - - +
210H GLY* 1.3 73.6 - - - +
212H LYS* 1.3 59.4 + - - +
574H THR* 4.7 5.6 - - + -
575H PHE* 4.1 12.1 - - + -
578H ALA* 3.7 20.9 - - + -
591H GLN* 4.6 3.1 - - - +
594H VAL* 4.3 8.7 - - + +
595H ASP* 2.9 28.1 + - - +
598H LEU* 3.2 37.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 212 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191H PHE* 3.7 3.3 - - - -
192H LEU* 3.0 36.0 + - - +
210H GLY 4.0 0.4 - - - -
211H LEU* 1.3 76.2 - - - +
213H SER* 1.3 64.6 + - - +
214H LEU* 4.1 0.3 - - - +
227H LYS* 3.5 27.5 - - + +
230H ALA* 6.2 1.1 - - + -
231H ILE* 4.2 19.0 - - + +
234H GLN* 3.6 25.6 - - - +
591H GLN* 5.8 4.9 - - + +
592H GLN* 4.0 27.3 + - - +
595H ASP* 3.6 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 213 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189H ARG* 4.8 8.3 - - - -
190H ASN 3.6 9.0 - - - -
191H PHE* 4.0 15.4 - - - -
212H LYS* 1.3 76.4 - - - +
214H LEU* 1.3 61.9 + - - +
215H ASP* 3.1 15.3 + - - +
216H PHE* 6.0 1.3 - - - -
227H LYS* 3.0 23.6 - - - -
591H GLN* 3.1 43.5 + - - +
----------------------------------------------------------
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