Contacts of the helix formed by residues 325 - 337 (chain D) in PDB entry 6XAV
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 SER 325 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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333C GLU* 3.8 27.3 - - - +
272D ARG* 4.2 4.7 + - - -
323D THR* 3.2 4.5 + - - -
324D GLY* 1.3 79.1 + - - +
326D LYS* 1.3 66.8 + - - +
327D MET* 3.3 20.3 + - - +
328D ASP* 3.5 25.0 + - - +
329D GLU* 3.7 8.7 + - - +
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Residues in contact with LYS 326 (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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286D THR* 6.5 0.4 - - + -
287D GLY* 4.9 9.2 - - - -
324D GLY 4.2 2.9 + - - +
325D SER* 1.3 70.2 + - - +
327D MET* 1.3 63.3 + - - +
329D GLU* 3.3 9.9 + - + +
330D VAL* 3.2 28.3 + - + +
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Residues in contact with MET 327 (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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286C THR* 5.4 4.7 - - - -
272D ARG* 3.4 46.7 - - + +
275D ASN* 4.8 11.9 - - - -
287D GLY* 3.3 30.3 + - - +
288D GLY* 4.3 12.6 - - - +
289D VAL* 3.7 14.1 - - + +
325D SER* 3.2 9.7 + - - +
326D LYS* 1.3 79.1 - - - +
328D ASP* 1.3 62.2 + - - +
330D VAL* 3.3 5.2 + - - +
331D ILE* 3.1 35.4 + - + +
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Residues in contact with ASP 328 (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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333C GLU* 4.3 0.3 - - - +
268D THR* 3.3 21.3 + - + +
272D ARG* 2.8 42.1 + - - -
320D LEU* 4.2 16.0 - - - +
321D ILE* 5.9 1.1 - - - -
323D THR* 2.8 35.4 + - - +
325D SER* 3.5 6.2 + - - +
326D LYS 3.3 0.2 - - - -
327D MET* 1.3 79.2 - - - +
329D GLU* 1.3 57.8 + - - +
331D ILE* 3.8 8.5 - - - +
332D TYR* 2.8 31.2 + - - +
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Residues in contact with GLU 329 (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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320D LEU 5.7 0.4 - - - -
321D ILE* 4.5 12.3 - - - +
322D ASP* 5.1 5.9 + - - +
325D SER 3.7 7.1 + - - +
326D LYS* 3.3 14.5 + - - +
327D MET 3.2 0.8 - - - -
328D ASP* 1.3 79.0 - - - +
330D VAL* 1.3 58.5 + - + +
332D TYR* 3.4 24.2 + - - +
333D GLU* 2.9 35.1 + - + +
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Residues in contact with VAL 330 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285D LEU* 6.4 2.2 - - + -
286D THR* 3.7 37.5 - - + +
287D GLY* 4.7 1.8 - - - -
289D VAL* 4.9 10.5 - - + -
294D LEU* 5.6 5.8 - - + -
326D LYS* 3.2 17.6 + - + +
327D MET* 3.3 7.4 + - - +
329D GLU* 1.3 75.7 - - + +
331D ILE* 1.3 60.7 + - - +
333D GLU* 3.8 4.7 - - - +
334D GLU* 2.9 32.8 + - + +
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Residues in contact with ILE 331 (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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267D ILE* 5.6 0.4 - - + -
268D THR* 4.7 20.2 - - + +
271D ALA* 3.7 28.9 - - + -
272D ARG* 5.0 3.8 - - + +
289D VAL* 4.6 10.1 - - + -
294D LEU* 4.2 17.7 - - + -
327D MET* 3.1 32.5 + - + +
328D ASP* 3.8 13.0 - - - +
330D VAL* 1.3 77.3 - - - +
332D TYR* 1.3 61.1 + - - +
334D GLU* 3.4 4.4 + - - +
335D PHE* 3.1 52.1 + - + -
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Residues in contact with TYR 332 (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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175D LEU* 6.2 3.1 - - + -
177D VAL* 3.6 27.3 - - + +
319D ALA* 4.0 17.5 - - + -
320D LEU 4.4 4.5 - - - +
321D ILE* 3.5 34.3 - - + +
328D ASP 2.8 18.7 + - - +
329D GLU* 3.6 16.8 - - - +
331D ILE* 1.3 77.8 - - - +
333D GLU* 1.3 76.3 + - - +
335D PHE* 3.8 3.7 - - - +
336D LYS* 3.0 52.4 + - + +
342D GLU* 5.7 0.6 - - + +
344D HIS* 3.4 22.9 - - - -
362D ARG* 5.4 2.1 + - - -
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Residues in contact with GLU 333 (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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329D GLU* 2.9 24.7 + - + +
330D VAL* 4.0 4.9 - - - +
332D TYR* 1.3 95.1 - - + +
334D GLU* 1.3 61.5 + - - +
336D LYS* 3.8 25.3 + - - +
337D GLY 4.3 2.3 + - - -
272E ARG* 4.4 19.5 + - - +
323E THR 3.7 19.6 - - - +
324E GLY 4.5 4.0 - - - +
325E SER* 3.7 25.4 + - - +
328E ASP* 5.5 0.2 - - - +
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Residues in contact with GLU 334 (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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294D LEU* 3.8 31.1 - - + +
298D LYS* 5.0 13.6 + - + +
330D VAL* 2.9 21.1 + - + +
331D ILE 3.9 3.6 - - - +
333D GLU* 1.3 78.9 - - - +
335D PHE* 1.3 70.2 + - + +
336D LYS 3.4 0.5 + - - -
337D GLY* 3.8 8.3 + - - -
338D THR* 3.9 8.3 + - - -
272E ARG* 4.6 17.8 + - - +
276E THR* 5.1 7.4 + - - +
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Residues in contact with PHE 335 (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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175D LEU* 3.5 23.6 - - + +
267D ILE* 3.6 36.6 - - + -
271D ALA* 4.7 2.0 - - + -
294D LEU* 4.1 22.7 - - + -
297D PRO* 3.9 31.9 - - + -
298D LYS* 4.0 29.2 - - + -
301D PHE* 5.0 6.5 - + + -
331D ILE* 3.1 37.9 + - + +
332D TYR* 3.8 3.6 - - - +
334D GLU* 1.3 83.9 - - + +
336D LYS* 1.3 63.9 + - - +
337D GLY 3.3 0.4 - - - -
338D THR* 3.3 26.0 + - - +
339D GLY 3.6 0.3 + - - -
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Residues in contact with LYS 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175D LEU* 4.6 7.4 - - - +
332D TYR* 3.0 44.6 + - + +
333D GLU* 3.9 28.6 + - - +
334D GLU 3.2 0.8 - - - -
335D PHE* 1.3 79.2 - - - +
337D GLY* 1.3 56.3 + - - +
338D THR 3.2 3.5 + - - -
339D GLY* 3.9 7.8 + - - +
342D GLU* 3.6 34.7 - - + +
344D HIS* 5.4 4.9 + - - -
212E ARG* 5.3 0.9 + - - -
323E THR 4.2 16.5 + - - +
324E GLY* 5.5 2.8 - - - -
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Residues in contact with GLY 337 (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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333D GLU 4.3 3.0 + - - -
334D GLU 3.8 7.3 + - - -
335D PHE 3.3 0.6 - - - -
336D LYS* 1.3 76.4 - - - +
338D THR* 1.3 59.4 + - - +
339D GLY 4.6 2.2 - - - -
210E ASP* 5.1 6.9 - - - +
212E ARG* 4.3 15.0 + - - +
232E PHE* 4.3 10.2 - - - -
269E ARG* 4.6 25.4 + - - -
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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