Contacts of the helix formed by residues 402 - 420 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A SER* 2.8 30.9 + - - -
14A ARG* 4.9 2.2 - - - +
208A VAL* 4.1 2.5 - - + -
209A GLY 3.0 18.3 + - - -
210A ASP* 3.1 22.1 + - - +
211A GLU 4.1 0.7 - - - -
212A GLY* 3.5 29.8 - - - +
401A ALA* 1.3 79.9 - - + +
403A SER* 1.3 59.3 + - - +
404A GLU* 2.8 33.7 + - - +
405A ARG* 2.9 20.0 + - + -
406A LEU* 3.2 9.0 + - - +
13B SER 2.8 16.0 + - - -
208B VAL* 3.5 24.4 - - - +
401B ALA* 4.5 3.0 - - - +
402B ARG* 3.5 41.0 - - - +
404B GLU* 3.7 8.5 - - - +
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Residues in contact with SER 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A GLU* 5.3 1.2 - - - -
402A ARG* 1.3 66.6 - - - +
404A GLU* 1.3 55.2 + - - +
405A ARG 3.0 4.9 - - - -
406A LEU* 3.8 8.7 - - - +
407A ALA* 2.8 32.1 + - - +
12B ASP* 4.4 1.9 - - - -
13B SER* 3.3 17.3 + - - -
378B THR* 3.7 9.9 - - - -
379B GLU* 4.0 22.3 + - - +
403B SER* 4.5 2.2 - - - -
404B GLU* 2.9 43.5 + - - +
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Residues in contact with GLU 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 3.2 19.9 - - - -
377A GLU* 3.5 14.2 - - + +
378A THR 3.6 17.0 - - - +
379A GLU* 5.0 0.2 - - - +
397A THR* 4.7 0.2 + - - -
402A ARG* 2.8 39.7 + - - +
403A SER* 1.3 77.4 - - - +
405A ARG* 1.3 87.9 + - - +
407A ALA 4.4 0.7 - - - -
408A LYS* 2.8 33.1 + - - +
402B ARG* 3.7 0.7 - - - -
403B SER* 2.9 43.7 + - - +
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Residues in contact with ARG 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A SER* 3.5 7.5 + - - -
210A ASP 3.0 18.1 + - - -
211A GLU* 3.7 21.4 - - - +
373A HIS* 2.7 34.4 + - - -
374A ARG 2.9 16.4 + - - -
375A SER 2.7 25.9 + - - -
377A GLU* 3.4 6.8 - - - +
397A THR* 3.2 25.2 - - - +
398A GLY* 3.8 7.6 - - - -
399A ALA 3.3 17.5 - - - +
401A ALA 3.4 17.5 - - - +
402A ARG* 2.9 7.4 + - + +
404A GLU* 1.3 104.4 + - + +
406A LEU* 1.3 64.5 + - - +
407A ALA 3.2 1.3 - - - -
408A LYS* 3.1 16.5 + - - +
409A LEU* 3.4 16.2 + - + +
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Residues in contact with LEU 406 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A LEU* 5.3 0.9 - - + -
400A PRO* 3.7 27.1 - - + +
401A ALA* 3.4 30.5 - - - +
402A ARG 3.2 15.5 + - - +
403A SER* 3.6 9.2 + - - +
405A ARG* 1.3 73.3 - - - +
407A ALA* 1.3 55.3 - - - +
409A LEU* 4.2 13.7 - - + -
410A ASN* 2.7 42.2 + - - +
11B TYR* 3.5 42.4 - - + +
12B ASP 3.1 20.9 - - - +
13B SER* 3.8 4.5 - - - -
379B GLU* 5.0 0.7 - - - +
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Residues in contact with ALA 407 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A GLU* 3.9 17.5 - - - +
381A THR* 3.3 29.5 - - + +
403A SER 2.8 23.6 + - - +
404A GLU 4.7 0.7 - - - +
405A ARG 3.2 0.6 - - - -
406A LEU* 1.3 72.6 - - - +
408A LYS* 1.3 61.2 + - + +
410A ASN* 3.9 1.4 - - - +
411A GLN* 3.1 20.6 + - - +
414A ARG* 4.4 1.4 + - - -
379B GLU* 3.6 30.2 + - + +
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Residues in contact with LYS 408 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377A GLU* 2.8 30.2 + - - -
378A THR 2.7 29.7 + - - -
380A ASP* 2.8 19.5 + - - +
381A THR* 4.4 8.7 - - - +
382A PHE 5.5 0.2 - - - +
383A ILE* 3.6 27.8 - - + -
384A ALA* 3.5 20.2 - - + +
395A ILE* 5.1 2.0 - - + -
397A THR* 3.4 31.4 - - + +
404A GLU 2.8 20.2 + - - +
405A ARG 3.1 4.8 + - - +
407A ALA* 1.3 77.6 - - + +
409A LEU* 1.3 60.9 + - - +
411A GLN* 3.2 1.8 + - - -
412A LEU* 3.0 27.4 + - - +
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Residues in contact with LEU 409 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A PRO* 4.0 26.5 - - + -
151A LEU* 3.9 21.8 - - + -
179A PHE* 3.5 22.0 - - + -
183A LEU* 3.8 25.8 - - + -
395A ILE* 5.3 0.2 - - + -
397A THR* 3.7 23.6 - - + -
398A GLY 4.6 1.1 - - - +
399A ALA 4.2 11.9 - - - +
400A PRO* 4.4 0.9 - - + -
405A ARG* 3.4 14.1 + - + +
406A LEU* 3.2 23.5 + - + +
408A LYS* 1.3 77.0 - - - +
410A ASN* 1.3 60.1 + - - +
412A LEU* 3.3 8.7 + - + -
413A LEU* 3.2 20.6 + - - +
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Residues in contact with ASN 410 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A LEU* 2.7 26.3 + - - +
407A ALA 3.9 0.7 - - - +
409A LEU* 1.3 70.7 - - - +
411A GLN* 1.3 64.8 + - - +
413A LEU* 3.2 11.2 + - - +
414A ARG* 3.1 36.3 + - - +
10B VAL* 3.5 17.2 - - + +
11B TYR* 2.8 57.6 + - - +
379B GLU* 3.0 32.1 + - - +
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Residues in contact with GLN 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A THR* 4.1 18.5 + - - +
384A ALA* 3.7 14.1 - - + -
385A ASP* 3.0 34.3 + - - +
407A ALA 3.1 19.8 + - - +
408A LYS 3.2 5.1 + - - +
410A ASN* 1.3 76.0 - - - +
412A LEU* 1.3 58.4 + - - +
414A ARG* 3.0 38.0 + - - +
415A ILE* 2.9 35.4 + - + +
31B ARG* 4.7 3.5 + - - -
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Residues in contact with LEU 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 3.9 5.5 - - + +
147A PRO* 3.8 17.7 - - + -
179A PHE* 3.4 43.3 - - + -
384A ALA* 3.4 31.2 - - + +
387A VAL* 3.9 7.0 - - + -
388A VAL* 3.8 18.8 - - + -
395A ILE* 4.0 20.4 - - + -
408A LYS 3.0 19.3 + - - +
409A LEU* 3.5 8.3 - - + +
410A ASN 3.2 0.2 - - - -
411A GLN* 1.3 72.8 - - - +
413A LEU* 1.3 55.3 + - - +
415A ILE* 3.2 4.1 + - + +
416A GLU* 2.8 36.6 + - - +
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Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A PHE* 3.8 12.9 - - + -
180A ALA* 3.7 36.6 - - + +
183A LEU* 4.0 8.5 - - + -
409A LEU 3.2 14.5 + - - +
410A ASN* 3.2 20.2 + - - +
412A LEU* 1.3 74.8 - - - +
414A ARG* 1.3 57.7 - - + +
416A GLU* 3.7 5.2 - - - +
417A GLU* 3.0 29.7 + - - +
8B ARG* 5.6 4.5 - - - -
9B SER 3.6 23.3 - - - +
10B VAL* 4.1 4.0 - - + -
11B TYR* 3.8 30.1 - - + -
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Residues in contact with ARG 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381A THR* 5.4 2.6 - - - +
407A ALA 4.4 2.8 + - - -
410A ASN* 3.1 22.6 + - - +
411A GLN* 3.0 50.9 + - - +
413A LEU* 1.3 72.1 - - - +
415A ILE* 1.3 63.0 + - - +
417A GLU* 3.4 7.2 + - - +
418A GLU* 3.0 30.1 + - - +
8B ARG* 4.1 20.6 + - - +
10B VAL* 4.3 2.0 - - - +
20B GLU* 2.7 42.4 + - - +
31B ARG* 3.4 36.7 - - - +
33B ILE* 4.0 4.9 - - - +
379B GLU* 3.6 20.8 + - - +
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Residues in contact with ILE 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A TYR* 3.7 28.5 - - + -
146A LEU* 4.7 2.7 - - + -
384A ALA 3.9 17.5 - - - +
385A ASP* 3.8 28.9 - - - +
388A VAL* 3.9 20.0 - - + -
411A GLN* 2.9 38.0 + - + +
412A LEU* 3.7 5.8 - - + +
414A ARG* 1.3 72.1 - - + +
416A GLU* 1.3 62.1 + - - +
418A GLU* 3.3 7.3 + - - +
419A LEU* 2.9 50.7 + - + +
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Residues in contact with GLU 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A LEU* 4.0 26.3 - - + +
178A THR* 3.5 13.7 - - - +
179A PHE* 2.9 31.5 + - + +
180A ALA* 2.7 34.5 + - - +
412A LEU 2.8 21.4 + - - +
413A LEU* 3.7 6.6 - - - +
415A ILE* 1.3 74.1 - - - +
417A GLU* 1.3 63.6 + - - +
419A LEU* 3.4 1.8 + - - +
420A GLY* 3.1 22.2 + - - +
423A ALA* 5.1 2.1 - - + +
425A PHE* 5.1 1.9 + - - +
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Residues in contact with GLU 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A LEU 3.0 17.2 + - - +
414A ARG 3.6 4.9 - - - +
416A GLU* 1.3 79.4 - - - +
418A GLU* 1.3 64.9 + - - +
420A GLY* 3.4 9.8 + - - -
6B TYR* 3.2 29.4 + - - +
8B ARG* 2.7 54.2 + - - +
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Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A PRO* 3.7 14.5 - - - +
130A TYR* 2.8 36.1 + - - +
414A ARG 3.0 18.2 + - - +
415A ILE* 3.5 5.9 - - - +
417A GLU* 1.3 80.8 + - - +
419A LEU* 1.3 62.5 + - - +
420A GLY* 3.4 0.7 + - - -
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Residues in contact with LEU 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A TYR* 3.9 21.1 - - + +
131A LYS* 5.0 5.8 - - - -
144A TYR* 3.3 53.6 - - + -
146A LEU* 4.0 7.0 - - + -
388A VAL* 4.1 2.7 - - + -
415A ILE* 2.9 38.5 + - + +
416A GLU 3.9 1.3 - - - +
417A GLU 3.3 0.2 - - - -
418A GLU* 1.3 76.5 - - - +
420A GLY* 1.3 65.4 + - - +
421A ASP 3.2 0.7 + - - -
422A ASN* 3.0 27.7 + - + +
423A ALA* 3.5 21.8 - - + -
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Residues in contact with GLY 420 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416A GLU 3.1 13.4 + - - +
417A GLU 3.4 8.0 + - - -
418A GLU 3.3 3.2 - - - -
419A LEU* 1.3 74.9 - - - +
421A ASP* 1.3 65.7 + - - +
422A ASN 3.3 1.0 + - - -
423A ALA* 3.4 17.2 + - - +
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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