Contacts of the strand formed by residues 174 - 179 (chain D) in PDB entry 3T79
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 LYS 174 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ILE* 4.1 5.8 - - + -
168D LEU* 3.6 0.5 - - - +
169D ASP* 2.5 45.6 + - + +
172D ASN* 3.6 26.5 - - + +
173D GLY* 1.3 79.9 - - - +
175D CYS* 1.3 64.6 + - - +
294D SER* 3.0 17.1 + - - -
295D ASP 2.6 28.1 + - - -
296D SER 3.8 8.6 + - - +
297D GLU 4.9 0.6 - - - -
298D ASN 3.2 13.5 + - - +
299D THR* 3.6 21.2 + - - -
304D ASP* 5.4 1.8 - - + +
315D LEU* 3.9 27.6 - - + -
316D GLN 3.1 5.4 - - - +
317D PRO* 4.0 2.8 - - - +
318D CYS 4.8 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 175 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ILE* 2.9 8.1 - - - -
168D LEU* 3.3 25.4 - - + -
174D LYS* 1.3 77.0 - - - +
176D GLY* 1.3 57.8 + - - +
188D VAL* 3.9 12.7 - - - +
189D PRO* 3.4 35.1 - - - +
191D PHE* 4.6 3.8 - - - -
315D LEU* 4.7 3.0 - - - +
316D GLN* 3.1 14.8 + - - +
317D PRO 4.1 2.0 - - - -
318D CYS* 3.7 29.2 - - + +
340D LEU* 3.9 10.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 176 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166D CYS* 3.6 2.4 - - - -
167D ILE* 2.9 34.1 + - - +
175D CYS* 1.3 76.3 - - - +
177D LEU* 1.3 65.2 + - - -
178D ALA* 5.6 0.2 - - - -
186D VAL* 5.5 3.1 - - - -
187D LEU 3.0 14.4 - - - -
188D VAL* 4.7 1.3 - - - -
189D PRO* 4.5 3.8 - - - -
199D ILE* 4.8 0.2 - - - -
340D LEU* 3.6 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D LEU* 4.3 22.4 - - + -
165D GLN 4.0 2.0 - - - -
166D CYS* 4.8 4.5 - - - +
176D GLY* 1.3 72.1 - - - +
178D ALA* 1.3 59.9 + - - +
185D PHE* 4.2 6.4 - - + +
186D VAL* 3.6 2.9 - - - +
187D LEU* 2.9 41.0 + - + +
199D ILE* 3.8 20.9 - - + -
202D MET* 3.3 34.1 - - + -
337D VAL* 3.9 35.7 - - + +
340D LEU* 3.4 29.2 - - + -
341D LEU* 4.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 178 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D LEU* 3.4 10.1 - - - +
165D GLN* 2.9 44.1 + - + +
167D ILE* 4.4 14.4 - - + -
176D GLY 4.1 0.2 - - - -
177D LEU* 1.3 74.6 - - - +
179D HIS* 1.3 61.3 + - - +
180D SER 4.3 0.4 - - - -
185D PHE* 3.6 4.3 - - - -
186D VAL* 3.7 20.2 - - + -
300D ILE* 4.3 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 179 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D VAL* 3.7 31.4 - - + +
163D ASP* 3.3 34.9 + - + +
164D LEU* 3.9 4.0 - - + -
165D GLN* 5.3 0.4 - - - -
178D ALA* 1.3 74.4 - - - +
180D SER* 1.3 60.9 + - - +
181D SER* 2.8 38.5 + - - -
183D PRO* 3.5 20.8 + - + +
184D ASN* 3.7 7.6 - - - +
185D PHE* 2.8 66.9 + + + +
300D ILE* 4.4 5.9 - - - +
----------------------------------------------------------
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