Contacts of the strand formed by residues 290 - 305 (chain D) in PDB entry 6QPA
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 290 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165D HIS* 3.9 32.1 - - + -
166D TRP 3.3 12.3 - - - +
167D VAL* 4.1 2.9 - - + -
168D MET* 3.7 11.8 - - - +
175D PHE* 4.0 14.1 - - + -
286D VAL* 3.2 22.0 - - + +
287D LEU* 3.4 22.0 + - + +
288D ALA 3.6 1.0 - - - -
289D HIS* 1.3 81.9 - - - +
291D ASP* 1.3 60.5 - - - +
292D LYS 3.9 8.7 - - - +
293D GLY 3.7 23.8 - - - +
294D PRO* 3.9 15.3 - - + -
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Residues in contact with ASP 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166D TRP* 2.7 16.2 + - + +
168D MET* 3.4 34.9 - - - +
169D ASP 4.3 2.1 + - - -
250D PRO* 3.5 29.9 - - + +
290D LEU* 1.3 72.9 - - - +
292D LYS* 1.3 59.0 + - + +
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Residues in contact with LYS 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164D ASP* 4.8 0.4 - - - -
165D HIS* 3.6 4.6 - - - -
166D TRP* 3.0 87.1 + - + +
290D LEU* 3.5 6.7 - - - +
291D ASP* 1.3 80.3 - - - +
293D GLY* 1.3 67.5 + - - +
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Residues in contact with GLY 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60D TYR* 5.2 4.7 - - - -
164D ASP 3.7 5.6 - - - -
287D LEU* 4.9 0.9 - - - +
290D LEU* 3.7 10.0 - - - +
292D LYS* 1.3 84.1 - - - +
294D PRO* 1.3 77.6 - - - +
295D TYR* 3.9 3.8 - - - -
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Residues in contact with PRO 294 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D MET* 3.6 32.0 - - + +
60D TYR* 3.7 8.7 + - - -
164D ASP 3.4 6.3 - - - +
165D HIS* 3.5 28.0 - - + +
282D HIS* 4.7 10.3 - - + -
287D LEU* 3.6 30.1 - - + -
290D LEU* 3.9 2.4 - - + -
293D GLY* 1.3 84.5 - - - +
295D TYR* 1.3 60.1 + - - +
296D TYR* 3.7 20.9 - - + -
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Residues in contact with TYR 295 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D GLN* 5.4 0.7 + - - -
53D ILE* 3.3 30.6 - - + +
54D HIS 5.6 0.7 - - - -
56D MET* 5.1 0.2 - - - -
60D TYR* 3.4 52.5 - + - +
162D ILE 3.3 3.3 - - - +
164D ASP* 2.8 47.5 + - + +
293D GLY* 5.0 3.1 - - - -
294D PRO* 1.3 74.6 - - - +
296D TYR* 1.3 64.1 + - - +
297D MET* 3.7 32.1 + - + +
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Residues in contact with TYR 296 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D ILE* 3.3 7.7 - - - +
54D HIS* 2.9 48.4 + - + +
56D MET* 4.6 14.8 - - + -
60D TYR* 5.6 0.2 - - - -
161D VAL* 3.2 29.8 - - + -
162D ILE 3.4 0.4 - - - -
163D GLY* 3.3 24.9 - - - -
165D HIS* 3.8 17.0 + + - -
255D VAL* 4.3 9.7 - - - +
257D ILE* 4.3 9.6 - - + +
269D LEU* 3.9 30.8 - - + +
282D HIS* 5.2 8.1 + + - -
294D PRO* 3.7 24.9 - - + -
295D TYR* 1.3 80.0 - - - +
297D MET* 1.3 61.5 + - - +
298D PHE* 4.6 1.1 - - + -
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Residues in contact with MET 297 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D LYS* 4.4 15.7 - - - +
50D GLN* 3.3 37.7 - - + +
52D GLY 3.7 3.8 - - - -
53D ILE* 4.6 0.2 - - + -
75D GLY* 4.6 1.6 - - - -
77D PHE* 4.3 19.1 - - + -
161D VAL* 3.4 4.2 - - - -
162D ILE* 3.0 36.2 + - - +
164D ASP* 6.3 2.2 - - - -
295D TYR* 3.7 31.0 - - + +
296D TYR* 1.3 72.9 - - - +
298D PHE* 1.3 60.6 + - - +
299D PHE* 3.5 34.3 - - + -
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Residues in contact with PHE 298 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50D GLN* 3.3 10.9 - - - +
51D THR* 2.8 35.8 + - - +
52D GLY* 2.8 18.9 + - - +
53D ILE 3.7 10.8 - - - -
54D HIS* 3.6 37.5 - + + -
65D VAL* 3.7 29.2 - - + +
159D THR* 4.2 13.9 - - + -
160D VAL 3.7 3.6 - - - -
161D VAL* 3.7 16.2 - - + -
262D PRO* 3.6 26.5 - - + -
265D ALA* 3.7 20.0 - - + -
266D HIS* 4.0 10.1 - - - -
269D LEU* 4.3 2.9 - - + -
296D TYR* 4.2 2.0 - - + -
297D MET* 1.3 75.9 - - - +
299D PHE* 1.3 59.8 + - - +
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Residues in contact with PHE 299 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 3.6 31.0 - - + -
49D LEU 3.2 5.4 - - - +
50D GLN* 3.5 28.7 - - + -
51D THR* 4.1 5.6 + - - -
75D GLY 4.3 2.9 - - - -
77D PHE* 3.8 34.8 - + - -
159D THR* 3.7 8.7 + - - +
160D VAL* 2.7 45.0 + - + +
162D ILE* 3.4 26.7 - - + -
297D MET* 3.5 51.6 - - + -
298D PHE* 1.3 76.2 - - - +
300D SER* 1.3 60.3 + - - +
301D PRO 4.2 0.2 - - - -
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Residues in contact with SER 300 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48D LEU* 3.5 2.6 - - - -
49D LEU* 2.7 35.9 + - - +
51D THR* 3.8 19.9 - - - +
156D SER 5.5 1.7 + - - -
158D ARG 4.4 4.3 + - - -
299D PHE* 1.3 75.3 - - - +
301D PRO* 1.3 68.9 + - - +
302D MET* 3.2 21.1 + - - -
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Residues in contact with PRO 301 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D GLN 3.3 8.3 - - - +
48D LEU* 3.8 15.7 - - + -
156D SER* 3.4 30.5 - - - +
158D ARG* 3.1 39.3 - - - +
160D VAL* 4.4 13.7 - - + -
299D PHE 4.1 3.1 - - - +
300D SER* 1.3 86.2 + - - +
302D MET* 1.3 66.1 + - - +
303D MET 3.6 0.4 - - - -
304D GLU* 3.8 24.5 - - + +
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Residues in contact with MET 302 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D TYR* 5.4 8.1 - - + -
25D MET* 5.8 6.3 - - + -
47D GLN* 2.8 34.2 + - + +
49D LEU* 3.9 38.4 - - + +
156D SER* 3.1 15.1 + - - -
300D SER* 4.0 21.8 - - - +
301D PRO* 1.3 72.2 - - - +
303D MET* 1.3 62.8 + - + +
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Residues in contact with MET 303 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25D MET 4.8 2.5 - - - +
26D MET* 6.5 0.4 - - - -
29D GLY* 4.3 21.1 - - - -
30D PRO* 4.4 17.9 - - + -
33D CSS 4.4 17.5 - - - -
45D PHE* 3.7 19.5 - - + -
47D GLN* 3.0 66.1 + - + +
156D SER* 4.1 0.9 - - - -
302D MET* 1.3 82.7 - - + +
304D GLU* 1.3 69.3 + - - +
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Residues in contact with GLU 304 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D PHE* 3.8 9.3 - - - +
46D GLU* 2.6 31.2 - - - +
129D ILE* 3.8 22.4 - - + +
155D SER* 3.5 7.8 + - - +
156D SER* 2.7 28.9 + - - +
158D ARG* 2.6 45.3 + - - -
301D PRO* 3.8 16.2 - - + +
303D MET* 1.3 80.4 - - - +
305D GLN* 1.3 59.3 + - - +
306D GLY 3.8 1.2 + - - +
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Residues in contact with GLN 305 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D PHE* 4.2 12.7 + - + -
43D LEU 3.6 7.1 + - - +
44D GLY* 3.4 18.8 - - - +
45D PHE* 3.1 59.9 + - + +
304D GLU* 1.3 72.1 - - - +
306D GLY* 1.3 57.2 + - - +
307D LEU* 3.0 34.5 + - + +
308D TRP* 3.3 6.8 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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