Contacts of the strand formed by residues 307 - 313 (chain D) in PDB entry 3GXM
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 GLY 307 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278D LEU 3.3 3.6 + - - -
279D LEU* 3.2 17.9 - - - +
280D MET 2.9 23.7 + - - -
305D VAL* 3.3 8.9 - - - +
306D HIS* 1.3 82.2 - - - +
308D ILE* 1.3 64.2 + - - -
334D THR* 3.6 6.5 - - - -
335D MET* 3.4 14.6 - - - -
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Residues in contact with ILE 308 (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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279D LEU* 4.9 0.7 - - - -
280D MET* 3.6 18.6 - - + -
281D LEU* 3.9 31.4 - - + -
288D LEU* 4.2 9.6 - - + -
292D ALA* 4.0 6.7 - - + -
296D LEU* 3.8 21.8 - - + -
307D GLY* 1.3 75.7 - - - -
309D ALA* 1.3 61.7 + - - +
310D VAL* 4.3 0.9 - - + -
327D THR* 3.7 26.0 - - + -
331D PHE* 5.2 2.5 - - + +
334D THR* 4.0 18.4 - - + +
335D MET* 2.8 12.5 + - - +
336D LEU* 3.6 20.4 - - + +
337D PHE* 2.9 28.6 + - - +
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Residues in contact with ALA 309 (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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231D THR* 4.4 4.5 - - + -
279D LEU* 4.1 20.6 - - + +
280D MET 2.7 15.8 + - - +
281D LEU* 3.4 10.6 - - - +
282D ASP* 2.7 35.7 + - + +
283D ASP 3.6 0.7 + - - -
307D GLY 4.2 0.8 + - - -
308D ILE* 1.3 71.7 - - - +
310D VAL* 1.3 61.6 + - - +
337D PHE* 3.1 8.7 - - + +
339D SER* 3.5 22.0 - - - +
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Residues in contact with VAL 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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281D LEU* 4.3 3.6 - - + -
283D ASP 3.3 6.7 - - - +
285D ARG* 4.4 15.5 - - + +
288D LEU* 3.7 29.8 - - + -
308D ILE* 4.3 2.2 - - + +
309D ALA* 1.3 79.2 - - - +
311D HIS* 1.3 67.3 + - - +
324D LEU* 4.3 16.4 - - + -
336D LEU* 4.1 16.6 - - + -
337D PHE 2.9 11.1 + - - +
338D ALA* 3.3 22.3 - - + +
339D SER* 2.9 23.0 + - - -
340D GLU 3.7 0.9 + - - -
370D ASN* 4.7 5.6 - - - +
375D VAL* 5.4 1.6 - - + -
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Residues in contact with HIS 311 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120D ARG* 4.0 2.0 - - - -
234D ASN* 3.2 20.8 + - - -
235D GLU* 2.9 32.8 - - + -
282D ASP* 2.9 39.2 + - - -
283D ASP* 2.8 14.6 + - - -
284D GLN* 3.5 17.3 - - - +
285D ARG* 3.6 13.2 + - - +
310D VAL* 1.3 77.7 - - - +
312D TRP* 1.3 76.5 + - - +
313D TYR* 4.4 3.1 - - + -
338D ALA* 6.1 0.4 - - - -
339D SER* 3.2 12.5 + - - -
340D GLU* 3.2 35.7 + - + +
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Residues in contact with TRP 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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317C LEU* 4.5 2.6 - - + +
284D GLN* 3.4 15.4 + - - -
285D ARG* 4.0 42.6 - - + +
286D LEU* 3.7 19.0 - - - +
310D VAL* 6.2 0.2 - - + -
311D HIS* 1.3 81.6 - - - +
313D TYR* 1.3 83.3 + - - +
314D LEU* 3.5 30.4 + - + +
316D PHE* 2.6 48.8 - - + +
317D LEU* 2.9 18.4 - - + -
318D ALA* 3.3 26.7 - - + +
338D ALA* 6.2 0.2 - - - +
340D GLU 2.8 12.3 + - - -
341D ALA* 3.2 28.6 - - + +
342D CYS 3.3 4.3 + - - -
366D SER* 5.8 1.3 - - - +
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Residues in contact with TYR 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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235D GLU* 2.7 32.2 + - - -
246D PHE* 6.1 0.9 - - - -
284D GLN* 2.8 39.5 - - - +
311D HIS* 4.5 6.7 - - + -
312D TRP* 1.3 91.2 - - + +
314D LEU* 1.3 64.9 + - - +
315D ASP* 3.2 4.0 + - + +
316D PHE* 3.3 32.4 + + + -
340D GLU* 3.8 12.3 + - - -
342D CYS* 3.7 31.0 - - - +
345D SER* 4.4 13.7 - - - +
381D TRP* 6.4 0.2 - + - -
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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