Contacts of the strand formed by residues 251 - 263 (chain T) in PDB entry 6MZL
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 251 (chain T).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172T VAL* 3.4 2.6 - - - +
173T ASN* 2.9 49.3 + - + +
175T GLY* 4.4 17.0 - - - -
249T LYS* 4.1 29.6 - - + -
250T PHE* 1.3 79.4 - - - +
252T ASP* 1.3 73.0 + - + +
253T PHE 3.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 252 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171T THR* 3.7 8.7 + - - +
172T VAL* 4.1 2.6 - - - -
173T ASN* 5.2 7.6 + - + +
250T PHE 4.2 0.8 + - - -
251T LEU* 1.3 80.9 - - - +
253T PHE* 1.3 67.8 + - - +
254T LYS* 3.6 5.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 253 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170T SER* 3.4 34.1 - - - -
171T THR 3.5 13.0 - - - -
172T VAL* 4.1 8.7 - - + -
227T GLU 5.0 1.6 - - - -
230T SER* 4.0 3.6 - - - -
231T ARG* 3.3 54.3 - - + +
234T ALA* 3.9 16.6 - - + -
250T PHE* 3.5 34.9 + + + -
251T LEU 3.4 2.4 - - - -
252T ASP* 1.3 77.7 - - - +
254T LYS* 1.3 62.1 + - - +
255T ILE* 4.1 23.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 254 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170T SER* 3.4 4.9 - - - -
171T THR* 3.1 30.2 + - - +
252T ASP 4.3 5.4 - - - +
253T PHE* 1.3 83.1 - - - +
255T ILE* 1.3 79.3 + - - +
256T GLN* 3.4 26.5 + - - +
316T LYS* 5.4 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 255 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168T ILE* 3.7 33.0 - - + -
169T VAL 3.8 2.7 - - - -
170T SER* 4.2 3.8 - - - -
227T GLU* 4.0 26.9 - - + -
230T SER* 5.4 0.4 - - - +
253T PHE* 4.1 22.9 - - + -
254T LYS* 1.3 83.6 - - - +
256T GLN* 1.3 63.0 + - - +
257T ASN 4.1 4.5 - - - +
258T MET* 4.0 17.3 - - + -
316T LYS* 3.7 34.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 256 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLU* 4.0 19.9 - - + +
81A LEU* 5.0 8.0 - - + +
169T VAL* 2.6 24.5 + - + +
171T THR* 3.3 42.7 + - + +
254T LYS* 3.4 39.3 + - - +
255T ILE* 1.3 74.6 - - - +
257T ASN* 1.3 60.2 + - + +
314T GLY 5.4 0.5 - - - +
315T ALA 4.5 0.4 - - - -
316T LYS* 2.5 45.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 257 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.3 30.6 - - - +
77A LEU* 3.3 23.6 - - - +
81A LEU* 3.6 20.1 - - + +
168T ILE* 3.5 0.3 - - - -
169T VAL* 2.8 44.7 + - + +
255T ILE* 3.8 2.1 - - - +
256T GLN* 1.3 81.2 - - - +
258T MET* 1.3 85.3 + - - +
313T THR* 3.8 1.1 + - - -
314T GLY* 3.3 25.0 + - - -
315T ALA 3.5 4.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 258 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU 5.4 0.2 - - - -
165T LEU* 3.8 33.9 - - + -
167T ASN 3.5 3.8 - - - +
168T ILE* 3.8 15.0 - - + -
227T GLU* 3.8 22.0 - - - +
255T ILE* 4.0 10.1 - - + -
257T ASN* 1.3 85.4 + - - +
259T VAL* 1.3 64.8 + - - +
312T LEU 3.7 0.7 - - - +
313T THR* 3.2 4.3 - - - -
314T GLY 3.0 25.3 + - - -
315T ALA* 3.1 21.2 + - + +
316T LYS 3.9 4.7 - - - +
317T VAL* 3.5 33.4 - - - +
318T ARG* 3.7 16.2 - - - -
321T ILE* 4.3 6.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 259 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 3.2 35.9 - - + +
43A PHE* 4.3 18.4 - - + +
165T LEU* 3.8 6.6 - - - +
166T GLN* 2.8 38.8 + - + -
167T ASN* 2.9 20.2 + - + +
257T ASN* 4.9 0.4 - - - +
258T MET* 1.3 73.4 - - - +
260T GLY* 1.3 62.7 + - - +
311T VAL* 4.0 16.4 - - + -
312T LEU 3.2 7.6 - - - +
313T THR* 3.3 27.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 260 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163T PRO* 5.3 1.3 - - - -
164T GLN 3.3 13.2 - - - -
165T LEU* 3.9 9.8 - - - +
166T GLN* 3.8 3.4 - - - -
258T MET 4.4 0.2 - - - -
259T VAL* 1.3 77.2 - - - +
261T SER* 1.3 60.9 + - - -
311T VAL* 3.4 6.8 - - - +
312T LEU* 2.9 35.9 + - - +
321T ILE* 4.6 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 261 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A LEU* 5.2 9.7 - - - +
163T PRO* 4.4 1.7 - - - +
164T GLN* 2.9 35.5 + - - +
166T GLN* 3.4 27.6 + - - +
260T GLY* 1.3 75.5 - - - -
262T CYS* 1.3 62.9 + - - +
309T LYS* 6.2 2.7 - - - -
310T VAL 3.2 11.4 - - - -
311T VAL* 4.1 15.9 - - - -
312T LEU* 4.9 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 262 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161T ILE* 3.9 11.7 - - + -
162T VAL 4.2 2.5 - - - +
163T PRO* 3.7 17.5 - - + -
164T GLN* 6.2 0.4 - - - -
261T SER* 1.3 78.7 - - - +
263T ASP* 1.3 62.2 + - - +
309T LYS* 3.1 11.3 - - - +
310T VAL* 2.8 43.3 + - - -
312T LEU* 4.1 7.6 - - - -
325T PHE* 3.5 41.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 263 (chain T).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161T ILE* 3.3 30.6 - - - +
262T CYS* 1.3 78.6 - - - +
264T VAL* 1.3 65.7 + - - +
265T LYS* 3.2 45.3 + - - +
307T SER 3.3 7.8 - - - +
308T GLY* 3.2 18.4 - - - -
309T LYS* 3.4 30.0 - - + -
----------------------------------------------------------
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