Contacts of the strand formed by residues 309 - 319 (chain D) in PDB entry 3M13
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 309 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226D GLY* 4.1 7.2 - - - -
227D PHE 3.7 14.6 - - - +
228D PHE* 4.0 18.2 - - + -
284D PHE* 3.5 32.3 - - + -
291D GLU* 4.1 18.2 - - + +
295D ARG* 3.3 21.1 - - - +
308D GLU* 1.3 78.9 + - - +
310D LYS* 1.3 61.1 + - - +
311D ARG 3.4 29.6 - - - +
312D GLY 5.2 0.2 - - - +
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Residues in contact with LYS 310 (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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227D PHE* 2.7 18.0 + - + +
228D PHE 4.3 1.6 - - - -
229D GLU* 2.6 57.6 + - - +
261D GLY 4.9 3.6 + - - -
262D CYS* 3.6 32.1 - - - +
263D GLY* 4.6 0.2 - - - -
308D GLU* 3.2 13.7 + - + +
309D LEU* 1.3 73.7 - - - +
311D ARG* 1.3 76.3 + - + +
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Residues in contact with ARG 311 (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 ASP* 5.3 3.2 + - - -
227D PHE* 2.8 66.1 + - + +
262D CYS* 5.2 8.9 + - - +
309D LEU* 3.4 14.1 - - - +
310D LYS* 1.3 98.7 + - - +
312D GLY* 1.3 65.9 + - - +
313D ALA* 6.3 0.2 - - - -
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Residues in contact with GLY 312 (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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225D VAL 3.2 11.9 - - - -
227D PHE* 4.3 4.3 - - - -
284D PHE* 3.5 31.7 - - - +
309D LEU* 5.2 0.4 - - - +
311D ARG* 1.3 83.2 - - - +
313D ALA* 1.3 60.5 - - - +
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Residues in contact with ALA 313 (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 HIS* 4.3 13.0 - - + -
46D GLY* 4.2 24.7 - - - -
224D VAL* 3.1 8.8 - - - +
225D VAL* 2.9 38.4 + - + +
227D PHE* 4.2 12.8 - - + -
284D PHE* 3.8 0.4 - - - -
312D GLY* 1.3 73.3 - - - +
314D VAL* 1.3 65.0 + - - +
315D CYS* 4.2 2.2 - - + -
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Residues in contact with VAL 314 (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 HIS* 2.9 19.3 + - - -
222D ARG* 3.6 39.7 - - + +
223D GLN 3.7 2.0 - - - -
224D VAL* 3.9 5.6 - - + -
280D ILE* 4.1 8.2 - - + +
281D ASN 3.7 7.9 - - - +
282D ARG* 3.5 46.0 + - - +
283D GLU 3.7 4.3 - - - +
284D PHE* 3.6 24.5 - - + +
313D ALA* 1.3 80.5 - - - +
315D CYS* 1.3 65.0 + - - +
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Residues in contact with CYS 315 (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 GLY 4.0 1.6 - - - -
43D SER* 3.6 14.6 - - - -
45D HIS* 3.6 22.9 - - + +
49D ARG* 3.5 17.5 - - - +
222D ARG* 3.7 1.9 - - - -
223D GLN 2.7 34.0 + - - +
225D VAL* 5.5 0.2 - - + -
280D ILE* 4.3 1.9 - - - +
313D ALA* 5.2 3.1 - - + -
314D VAL* 1.3 78.3 - - - +
316D MET* 1.3 65.5 + - - +
400D FAD 2.3 59.9 - - + -
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Residues in contact with MET 316 (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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41D ASN 3.2 26.9 - - - +
42D GLY* 3.7 10.1 + - - +
43D SER* 2.5 37.9 + - - +
203D ALA* 3.7 22.4 - - + -
204D TRP* 3.7 16.2 - - + -
221D TYR 3.1 10.3 - - - +
275D ILE* 3.6 17.0 - - + -
277D PRO* 3.6 23.3 - - + -
280D ILE* 3.5 26.9 - - + -
282D ARG* 4.1 7.2 - - - +
315D CYS* 1.3 79.2 - - - +
317D TYR* 1.4 62.4 + - - +
400D FAD 3.3 9.4 - - - +
405D CL 4.2 0.7 - - - +
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Residues in contact with TYR 317 (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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220D PRO* 3.2 4.7 - - - +
221D TYR* 2.8 36.5 + - + +
223D GLN* 3.5 35.4 + - + +
254D TYR* 3.4 21.7 + - - -
269D HIS* 2.6 53.5 + + - -
316D MET* 1.4 73.6 - - - +
318D THR* 1.3 64.8 + - - +
319D LYS* 4.0 21.5 - - + -
343D SER 4.4 2.2 - - - -
344D GLY* 3.3 25.8 + - - +
400D FAD 3.2 41.7 - + + -
405D CL 3.6 4.3 - - - -
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Residues in contact with THR 318 (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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43D SER* 4.7 3.5 + - - -
202D GLY* 3.8 15.2 - - - +
203D ALA* 3.1 32.5 + - - +
206D SER* 4.5 5.4 - - - -
218D LEU* 4.0 33.0 - - + -
219D GLN 3.5 6.3 - - - +
220D PRO* 4.4 5.6 - - - +
317D TYR* 1.3 78.1 + - - +
319D LYS* 1.3 59.0 + - - +
341D GLY* 3.2 19.8 - - - +
342D PHE 4.9 0.2 - - - -
343D SER 3.1 18.0 + - - -
405D CL 3.3 11.4 - - - +
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Residues in contact with LYS 319 (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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217D PRO 4.1 0.2 - - - +
218D LEU* 3.3 7.8 - - - -
219D GLN* 2.9 35.1 + - + +
221D TYR* 3.5 48.2 + - + +
223D GLN* 5.2 1.6 - - - -
269D HIS* 4.7 7.5 + - - -
270D THR* 4.4 15.8 + - - +
317D TYR* 4.3 22.0 - - + -
318D THR* 1.3 74.3 - - - +
320D THR* 1.3 67.5 + - - +
323D GLU* 3.4 31.6 + - + +
343D SER* 3.4 18.2 - - - +
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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