Contacts of the strand formed by residues 243 - 250 (chain D) in PDB entry 1ML3
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 243 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320C LEU* 3.8 7.3 - - - +
171D LEU* 4.6 7.9 - - + -
175D VAL* 4.1 28.3 - - + -
185D VAL* 3.5 29.4 - - + -
188D GLY* 3.3 19.3 - - - +
229D ALA* 3.7 16.8 - - + +
230D LYS* 4.0 17.3 - - - +
232D VAL* 4.3 17.0 - - + -
239D THR* 3.8 16.1 + - - +
241D GLY* 4.7 3.3 + - - +
242D LYS* 1.3 110.2 + - + +
244D THR* 1.3 67.1 + - - +
260D LEU* 5.2 7.2 - - + -
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Residues in contact with THR 244 (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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317C GLN 5.8 0.2 + - - -
318C ASN* 3.9 10.2 + - - +
319C ASN 3.9 4.1 + - - +
320C LEU* 3.7 27.1 - - + +
321C PRO* 5.8 2.2 - - - -
188D GLY 3.6 1.6 + - - -
189D LEU* 3.2 30.7 - - + -
190D MET 3.1 19.2 + - - -
226D THR 4.7 5.1 + - - -
229D ALA* 3.4 19.7 - - - +
230D LYS* 4.4 10.8 - - - +
243D LEU* 1.3 78.1 - - - +
245D GLY* 1.3 67.3 + - - +
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Residues in contact with GLY 245 (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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318C ASN* 3.4 19.2 + - - +
328C LYS* 4.8 2.0 - - - -
189D LEU* 4.7 2.0 - - - -
190D MET* 3.0 18.8 - - - -
226D THR* 3.4 25.3 + - - +
229D ALA* 3.9 3.4 - - - +
244D THR* 1.3 88.2 + - - +
246D MET* 1.3 60.8 + - - -
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Residues in contact with MET 246 (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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259C ASP* 4.7 0.4 - - - +
314C ALA* 4.3 7.9 - - + -
318C ASN* 3.2 36.3 - - + +
328C LYS* 3.7 16.8 - - + +
330C VAL* 3.7 24.0 - - + -
190D MET* 3.0 4.6 + - - +
191D THR* 3.3 18.7 - - - +
192D THR* 3.2 24.4 + - - +
223D PRO* 4.0 14.1 - - + -
224D SER 3.6 6.7 - - - +
226D THR* 3.6 6.4 - - - +
245D GLY* 1.3 73.1 - - - -
247D SER* 1.3 74.4 + - - +
248D PHE* 3.6 34.3 - - + -
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Residues in contact with SER 247 (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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192D THR* 3.4 25.5 + - - +
194D HIS* 3.6 15.6 - - - +
222D ILE 4.5 0.2 - - - -
223D PRO* 3.3 3.8 - - - +
224D SER* 2.6 51.7 + - - -
226D THR* 4.2 10.8 - - - -
246D MET* 1.3 77.2 - - - +
248D PHE* 1.3 68.2 + - - +
249D ARG* 4.1 10.8 + - - +
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Residues in contact with PHE 248 (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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193C ILE* 3.9 28.0 - - + -
257C VAL* 4.2 22.7 - - + -
259C ASP* 4.4 9.6 - - + -
330C VAL* 4.3 15.5 - - + -
332C TRP* 5.0 0.2 - + - -
191D THR* 3.4 33.0 - - + -
192D THR 2.9 8.6 + - - +
193D ILE* 3.5 8.0 - - + -
194D HIS 2.8 25.8 + - - +
221D ILE* 3.9 22.0 - - + -
222D ILE 3.5 2.0 - - - -
223D PRO* 3.9 25.4 - - + -
246D MET* 3.6 31.9 - - + -
247D SER* 1.3 75.0 + - - +
249D ARG* 1.3 64.2 + - - +
250D VAL* 3.5 5.2 + - + +
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Residues in contact with ARG 249 (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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194D HIS* 3.1 39.1 + - - +
195D SER 3.7 0.9 - - - -
196D TYR* 5.0 0.4 - - + -
197D THR* 3.3 19.1 + - - +
199D THR* 4.3 2.0 + - - -
200D GLN* 2.7 61.6 - - - +
217D ALA 5.6 0.9 - - - +
220D ASN 3.3 5.6 - - - +
221D ILE* 3.5 2.1 - - - -
222D ILE* 2.8 52.0 + - + +
224D SER* 4.9 12.1 + - - -
247D SER* 4.1 8.5 + - - +
248D PHE* 1.3 70.9 - - - +
250D VAL* 1.3 58.9 + - - +
3166D CYX 3.0 44.1 + - - +
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Residues in contact with VAL 250 (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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193C ILE* 4.1 13.2 - - + -
221C ILE* 3.7 34.5 - - + -
250C VAL* 4.1 17.3 - - + -
251C PRO* 5.1 0.7 - - + -
193D ILE* 3.7 16.2 - - + -
194D HIS 2.9 14.4 + - - +
195D SER* 4.0 0.3 - - - -
196D TYR* 3.4 22.2 + - - +
217D ALA 4.4 1.8 - - - -
220D ASN 3.9 1.6 - - - -
221D ILE* 4.4 8.7 - - + -
248D PHE* 3.7 11.0 - - + +
249D ARG* 1.3 79.9 - - - +
251D PRO* 1.3 72.3 - - + +
252D THR* 2.9 14.7 + - - +
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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