Contacts of the helix formed by residues 402 - 420 (chain B) in PDB entry 2XGZ
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 ARG 402 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A SER 2.9 13.1 + - - -
208A VAL* 3.6 25.3 - - - +
401A ALA* 4.5 3.6 - - - +
402A ARG* 3.6 41.2 - - + +
404A GLU* 3.7 7.0 - - - +
13B SER* 2.9 30.3 + - - -
14B ARG* 4.9 4.0 - - - +
208B VAL* 4.2 3.8 - - + -
209B GLY 3.0 25.4 + - - -
210B ASP* 3.1 27.4 + - - +
211B GLU 4.2 0.7 - - - -
212B GLY* 3.6 14.8 - - - +
401B ALA* 1.3 78.0 - - - +
403B SER* 1.3 60.1 + - - +
404B GLU* 2.7 35.8 + - - +
405B ARG* 2.9 17.8 + - + -
406B LEU* 3.1 11.9 + - - +
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Residues in contact with SER 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR 5.1 0.2 + - - -
12A ASP 4.4 1.6 - - - -
13A SER* 3.4 16.8 + - - -
377A GLU 3.7 5.5 + - - -
378A THR* 3.7 4.0 - - - -
379A GLU* 4.2 19.4 + - - +
403A SER* 4.5 3.1 - - - -
404A GLU* 2.9 44.7 + - - +
379B GLU* 5.2 0.8 - - - -
402B ARG* 1.3 67.9 - - - +
404B GLU* 1.3 58.7 + - - +
405B ARG 3.0 1.8 - - - -
406B LEU* 3.9 9.9 - - - +
407B ALA* 2.7 34.8 + - - +
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Residues in contact with GLU 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402A ARG* 3.7 0.7 - - - -
403A SER* 2.9 42.4 + - - +
13B SER* 3.3 19.3 - - - -
210B ASP 3.4 0.2 - - - +
377B GLU* 3.5 11.4 - - + +
378B THR 3.5 16.4 - - - +
397B THR* 4.7 0.2 + - - -
402B ARG* 2.7 40.4 + - - +
403B SER* 1.3 76.7 - - - +
405B ARG* 1.3 90.9 + - - +
407B ALA* 4.7 0.4 - - - -
408B LYS* 2.9 32.7 + - - +
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Residues in contact with ARG 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER* 3.5 7.7 + - - -
210B ASP 3.0 18.5 + - - -
211B GLU* 3.7 21.1 - - - +
373B HIS* 2.8 27.5 + - - -
374B ARG 2.8 22.4 + - - -
375B SER 2.7 26.9 + - - -
377B GLU* 3.5 8.4 - - - +
397B THR 3.2 26.3 - - - +
398B GLY* 3.7 7.4 - - - -
399B ALA 3.4 17.7 - - - +
401B ALA 3.4 16.6 - - - +
402B ARG* 2.9 6.2 + - + +
404B GLU* 1.3 104.6 + - - +
406B LEU* 1.3 66.0 + - - +
407B ALA 3.2 1.1 - - - -
408B LYS* 3.2 17.3 + - - +
409B LEU* 3.4 16.2 + - + +
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Residues in contact with LEU 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TYR* 3.4 42.6 - - + +
12A ASP 3.0 22.0 - - - +
13A SER* 3.9 2.9 - - - -
15A GLY* 4.7 0.2 - - - -
183B LEU* 5.3 0.9 - - + -
400B PRO* 3.7 28.7 - - + +
401B ALA* 3.6 22.9 - - - +
402B ARG 3.1 23.9 + - - +
403B SER* 4.0 8.3 - - - +
405B ARG* 1.3 72.3 - - - +
407B ALA* 1.3 57.2 + - - +
409B LEU* 3.7 13.9 - - + -
410B ASN* 2.7 39.9 + - - +
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Residues in contact with ALA 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A GLU* 3.9 26.6 - - + -
379B GLU* 3.9 16.8 - - - +
381B THR* 3.4 22.3 - - + +
403B SER* 2.7 24.9 + - - +
404B GLU 4.5 0.7 - - - +
405B ARG 3.2 0.2 - - - -
406B LEU* 1.3 72.1 - - - +
408B LYS* 1.3 63.5 + - + +
410B ASN* 3.8 1.6 - - - +
411B GLN* 3.0 28.2 + - - +
414B ARG* 4.5 1.6 + - - -
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Residues in contact with LYS 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377B GLU* 2.8 27.5 + - - -
378B THR 2.7 29.1 + - - -
380B ASP 2.9 22.0 + - - +
381B THR* 4.4 5.2 - - - -
383B ILE* 3.7 29.2 - - + -
384B ALA* 3.5 18.0 - - + +
395B ILE* 5.2 1.1 - - + -
397B THR* 3.4 26.9 - - + +
404B GLU 2.9 21.0 + - - +
405B ARG 3.2 6.7 + - - +
406B LEU 3.1 0.6 - - - -
407B ALA* 1.3 77.3 - - + +
409B LEU* 1.3 59.7 + - - +
411B GLN* 3.2 1.4 + - - -
412B LEU* 2.9 34.5 + - - +
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B PRO* 4.0 25.8 - - + -
151B LEU* 3.9 20.4 - - + -
179B PHE* 3.4 24.4 - - + -
183B LEU* 3.9 26.9 - - + -
397B THR* 3.6 23.1 - - + -
398B GLY 4.6 2.7 - - - +
399B ALA 4.0 16.6 - - - +
400B PRO* 4.3 1.3 - - + -
405B ARG 3.6 14.1 - - - +
406B LEU* 3.2 20.1 + - + +
408B LYS* 1.3 76.8 - - - +
410B ASN* 1.3 63.0 + - - +
412B LEU* 3.2 6.2 + - + -
413B LEU* 3.1 19.2 + - - +
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Residues in contact with ASN 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 3.4 16.8 - - + +
11A TYR* 2.8 56.8 + - - +
379A GLU* 3.0 33.6 + - - +
406B LEU* 2.7 24.7 + - - +
407B ALA 3.8 1.3 - - - +
409B LEU* 1.3 70.1 - - - +
411B GLN* 1.3 65.0 + - - +
413B LEU* 3.1 11.3 + - - +
414B ARG* 3.1 35.8 + - - +
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Residues in contact with GLN 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A ARG* 4.8 4.2 + - - -
130B TYR* 5.6 0.4 - - - -
381B THR* 3.9 19.1 + - - +
384B ALA* 3.7 14.4 - - + -
385B ASP* 3.0 34.9 + - - +
407B ALA 3.0 20.2 + - - +
408B LYS 3.2 5.3 + - - +
410B ASN* 1.3 75.9 - - - +
412B LEU* 1.3 57.1 + - - +
414B ARG* 3.3 29.2 + - - +
415B ILE* 2.9 38.3 + - + +
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Residues in contact with LEU 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LEU* 3.7 8.0 - - + +
147B PRO* 3.8 23.3 - - + -
179B PHE* 3.4 38.8 - - + -
384B ALA* 3.7 17.5 - - + +
387B VAL* 4.0 2.0 - - + -
388B VAL* 3.6 31.2 - - + -
395B ILE* 4.0 22.7 - - + -
408B LYS 2.9 19.7 + - - +
409B LEU* 3.4 8.5 - - + +
410B ASN 3.2 0.2 - - - -
411B GLN* 1.3 73.6 - - - +
413B LEU* 1.3 60.7 + - - +
415B ILE* 4.4 3.4 - - + -
416B GLU* 2.8 31.0 + - - +
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Residues in contact with LEU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 5.6 3.6 - - - -
9A SER 3.7 22.9 - - - +
10A VAL* 4.1 3.8 - - + -
11A TYR* 3.8 30.1 - - + -
179B PHE* 3.7 12.5 - - + -
180B ALA* 3.7 37.2 - - + +
183B LEU* 4.0 8.5 - - + -
409B LEU 3.1 15.7 + - - +
410B ASN* 3.2 19.5 - - - +
412B LEU* 1.3 74.7 - - - +
414B ARG* 1.3 59.4 + - + +
416B GLU* 3.3 5.5 + - - +
417B GLU* 3.0 30.0 + - - +
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Residues in contact with ARG 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 3.7 28.0 + - - +
10A VAL* 4.3 3.1 - - + +
20A GLU* 2.8 38.5 + - - -
31A ARG* 3.3 39.6 - - - +
33A ILE* 4.2 3.4 - - - +
379A GLU* 3.4 24.2 + - - +
381B THR* 5.5 2.2 - - - +
407B ALA 4.5 1.6 + - - -
410B ASN* 3.1 18.4 + - - +
411B GLN* 3.3 51.3 + - - +
413B LEU* 1.3 73.0 - - - +
415B ILE* 1.3 66.9 + - + +
417B GLU* 3.3 8.0 + - - +
418B GLU* 3.0 25.4 + - - +
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Residues in contact with ILE 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B TYR* 3.7 28.0 - - + -
146B LEU* 4.5 3.4 - - + -
384B ALA 4.1 16.8 - - - +
385B ASP* 4.0 21.3 - - - +
388B VAL* 4.1 22.0 - - + -
411B GLN* 2.9 41.6 + - + +
412B LEU* 3.3 6.5 + - + +
414B ARG* 1.3 75.8 - - + +
416B GLU* 1.3 64.7 + - - +
418B GLU* 3.3 7.5 + - - +
419B LEU* 3.0 42.8 + - + +
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Residues in contact with GLU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B LEU* 3.9 28.7 - - + +
178B THR* 3.5 14.4 - - - +
179B PHE* 2.7 31.9 + - + +
180B ALA* 2.9 32.4 + - - +
412B LEU 2.8 17.2 + - - +
413B LEU* 3.6 6.6 - - - +
414B ARG 3.3 0.2 - - - -
415B ILE* 1.3 79.0 - - - +
417B GLU* 1.3 63.5 + - - +
419B LEU* 3.4 2.2 + - - +
420B GLY* 3.0 23.4 + - - +
423B ALA* 5.2 2.4 - - + +
424B VAL 5.7 0.5 - - - -
425B PHE* 4.8 3.5 + - - +
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Residues in contact with GLU 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A TYR* 3.1 30.6 + - - +
8A ARG* 2.6 54.0 + - - +
413B LEU 3.0 16.2 + - - +
414B ARG 3.3 3.8 + - - +
416B GLU* 1.3 78.0 - - - +
418B GLU* 1.3 67.2 + - - +
420B GLY* 3.4 9.6 + - - -
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Residues in contact with GLU 418 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B PRO* 3.7 14.5 - - - +
130B TYR* 2.7 36.6 + - - +
414B ARG 3.0 16.5 + - - +
415B ILE* 3.6 5.6 - - - +
417B GLU* 1.3 82.4 - - - +
419B LEU* 1.3 61.0 + - - +
420B GLY* 3.5 0.3 + - - -
422B ASN* 5.1 1.6 + - - -
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Residues in contact with LEU 419 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B TYR* 3.7 27.8 - - + +
131B LYS* 4.6 7.4 - - - -
144B TYR* 3.5 42.0 - - + -
146B LEU* 4.2 4.5 - - + -
388B VAL* 4.5 2.0 - - + -
415B ILE* 3.0 37.6 + - + +
416B GLU 4.0 1.3 - - - +
418B GLU* 1.3 76.7 - - - +
420B GLY* 1.3 65.3 + - - +
421B ASP 3.2 0.7 + - - -
422B ASN* 2.9 39.4 + - + +
423B ALA* 3.6 29.4 - - + +
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Residues in contact with GLY 420 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B GLU* 3.0 17.2 + - - +
417B GLU 3.4 7.2 + - - -
418B GLU 3.4 3.4 - - - -
419B LEU* 1.3 72.9 - - - +
421B ASP* 1.3 60.0 + - - -
422B ASN 3.1 5.4 + - - -
423B ALA* 3.2 19.8 + - - +
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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
------------------------------------------------------------
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