Contacts of the helix formed by residues 425 - 442 (chain B) in PDB entry 4XZC
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 ASN 425 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156B TYR* 3.7 19.0 - - - -
157B LYS 3.1 19.9 + - - +
158B VAL* 3.9 4.0 - - - +
159B PRO* 3.9 15.0 - - + +
418B LYS 3.5 0.9 - - - +
419B ILE* 3.2 37.7 + - - +
420B ASP 3.1 8.9 + - - -
421B THR* 4.7 0.6 - - - +
424B GLY* 1.3 80.8 - - - +
426B PRO* 1.3 67.6 - - - +
428B ALA* 3.0 33.3 + - + +
429B LYS* 3.1 16.6 + - - +
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Residues in contact with PRO 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B LEU* 3.5 30.1 - - + +
40B LEU* 4.0 31.8 - - + +
417B TYR* 4.1 11.4 - - + -
418B LYS* 3.3 21.5 - - + +
423B ALA* 3.3 27.4 - - + +
424B GLY 3.5 0.4 - - - -
425B ASN* 1.3 86.0 - - - +
427B CYS* 1.3 63.2 + - - +
429B LYS* 3.3 4.7 + - + +
430B GLU* 3.1 27.7 + - - +
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Residues in contact with CYS 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414B LEU* 3.8 18.7 - - - +
415B LEU* 4.5 11.4 - - - -
417B TYR* 3.2 24.7 - - + +
418B LYS 3.0 19.8 + - - +
419B ILE* 3.4 19.5 - - + -
426B PRO* 1.3 77.8 - - - +
428B ALA* 1.3 60.3 + - - +
430B GLU* 3.6 3.1 + - - +
431B ILE* 3.0 44.7 + - - +
459B SER* 3.9 11.4 - - - -
463B LYS 6.1 0.2 - - - -
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Residues in contact with ALA 428 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B TYR* 4.0 9.4 + - + +
158B VAL* 4.2 21.3 - - + -
162B TYR* 5.3 0.4 - - - -
166B VAL* 4.9 6.3 - - + -
425B ASN* 3.0 36.5 + - + +
427B CYS* 1.3 74.9 - - - +
429B LYS* 1.3 66.7 + - + +
431B ILE* 3.1 13.3 + - + +
432B VAL* 3.0 27.8 + - - +
456B LEU* 5.6 1.3 - - + -
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Residues in contact with LYS 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.3 33.6 - - + +
159B PRO* 5.3 2.5 - - + -
161B GLU* 4.7 9.2 - - - -
162B TYR* 3.4 48.1 - - + +
423B ALA 3.8 13.7 + - - -
424B GLY* 3.2 25.7 + - - +
425B ASN 3.1 11.0 + - - +
426B PRO* 3.3 8.5 + - - +
428B ALA* 1.3 78.2 - - + +
430B GLU* 1.3 62.2 + - - +
432B VAL* 3.4 4.3 + - - +
433B GLN* 3.1 29.8 + - - +
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Residues in contact with GLU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 3.1 29.3 - - + +
41B PRO* 2.8 35.8 - - - +
43B LEU* 4.0 8.0 - - - +
70B ALA* 3.4 22.8 - - - +
414B LEU* 3.5 21.5 - - + -
417B TYR* 3.6 20.0 - - + -
426B PRO 3.1 7.8 + - - +
427B CYS 4.0 0.9 - - - +
428B ALA 3.3 0.2 - - - -
429B LYS* 1.3 75.1 - - - +
431B ILE* 1.3 67.5 + - - +
433B GLN* 3.0 20.0 + - - +
434B LEU* 2.9 29.7 + - + +
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Residues in contact with ILE 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B TYR* 4.3 2.5 - - - +
169B MET* 3.8 15.9 - - + -
414B LEU* 4.1 18.4 - - + +
415B LEU* 6.2 0.2 - - + -
427B CYS* 3.0 37.7 - - - +
428B ALA* 3.1 10.5 + - - +
430B GLU* 1.3 75.8 - - - +
432B VAL* 1.3 53.7 + - + +
434B LEU* 3.4 7.3 + - - +
435B PHE* 2.7 33.8 + - - +
452B SER* 3.1 31.8 - - - +
455B LEU* 4.6 6.1 - - + +
456B LEU* 3.9 36.6 - - + +
459B SER* 4.7 0.4 - - - -
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Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B TYR* 3.4 36.6 - - + -
165B GLU* 3.5 21.5 - - + +
166B VAL* 4.2 15.7 - - + -
169B MET* 4.5 10.5 - - - -
428B ALA 3.0 14.5 + - - +
429B LYS 3.4 8.5 - - - +
430B GLU 3.2 0.2 - - - -
431B ILE* 1.3 75.5 - - + +
433B GLN* 1.3 53.6 + - - +
435B PHE* 2.8 11.0 + - + +
436B ARG* 2.6 60.4 + - + +
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Residues in contact with GLN 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B LEU* 5.1 2.4 - - - +
41B PRO 3.7 6.7 + - - -
42B ASP* 3.9 6.4 - - - +
43B LEU* 3.2 43.3 + - + +
44B SER 4.7 0.7 + - - -
47B GLU* 5.1 2.9 - - - +
162B TYR* 4.3 14.5 + - + -
429B LYS* 3.1 21.7 + - - +
430B GLU* 3.0 28.3 + - - +
432B VAL* 1.3 74.2 - - + +
434B LEU* 1.3 57.5 + - - +
436B ARG* 3.2 25.1 + - - +
437B ILE* 2.8 37.3 + - - +
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Residues in contact with LEU 434 (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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43B LEU* 3.9 13.0 - - + -
63B TYR* 3.5 30.2 - - + +
66B ALA* 4.3 2.0 - - + -
67B MET* 3.9 43.5 - - + +
70B ALA* 4.0 14.1 - - + -
414B LEU* 3.6 28.7 - - + -
430B GLU 2.9 19.8 + - - +
431B ILE* 3.6 4.7 - - - +
433B GLN* 1.3 75.3 - - - +
435B PHE* 1.3 58.2 + - - +
437B ILE* 4.0 5.0 - - + +
438B GLN* 3.1 32.2 + - - +
452B SER* 4.2 11.2 - - - -
455B LEU* 5.2 0.9 - - + -
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Residues in contact with PHE 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B GLU* 4.2 13.2 - - + -
168B GLU* 3.9 28.5 - - + -
169B MET* 3.4 46.2 - - + -
172B ASP* 5.9 1.3 - - + -
431B ILE 2.7 15.7 + - - +
432B VAL* 2.8 12.9 + - - +
434B LEU* 1.3 75.6 - - - +
436B ARG* 1.3 58.8 + - - -
438B GLN* 3.2 2.5 + - - +
439B LYS* 2.8 52.2 + - + +
444B LEU* 3.6 28.5 - - + -
450B VAL* 4.9 0.7 - - + -
452B SER* 3.6 16.6 - - - -
453B GLU* 3.9 14.4 - - - -
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Residues in contact with ARG 436 (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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47B GLU* 3.2 35.1 + - - +
161B GLU* 4.9 4.8 + - - +
162B TYR* 3.2 33.4 + - - -
165B GLU* 2.8 41.7 + - - +
432B VAL* 2.6 26.8 + - + +
433B GLN* 3.2 18.5 + - - +
435B PHE* 1.3 73.1 - - - +
437B ILE* 1.3 63.9 + - - +
439B LYS* 2.9 27.0 + - - +
440B ALA* 3.0 13.0 + - - +
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Residues in contact with ILE 437 (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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43B LEU* 3.7 28.0 - - + +
46B PHE* 3.7 12.8 - - + +
47B GLU* 3.9 23.5 - - + +
50B MET* 3.2 45.9 - - + +
63B TYR* 4.1 16.6 - - + -
66B ALA* 3.4 27.1 - - + -
433B GLN 2.8 22.2 + - - +
434B LEU* 4.0 5.8 - - - +
436B ARG* 1.3 71.7 - - - +
438B GLN* 1.3 62.8 + - - +
440B ALA* 3.1 13.7 + - - -
441B GLY 3.7 0.2 + - - -
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Residues in contact with GLN 438 (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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63B TYR* 4.1 28.2 + - + -
434B LEU 3.1 16.9 + - - +
435B PHE* 3.4 4.7 - - - +
436B ARG 3.1 0.2 - - - -
437B ILE* 1.3 75.9 - - - +
439B LYS* 1.3 64.2 + - - +
440B ALA 3.3 0.5 + - - -
442B PHE* 3.3 43.0 + - + +
444B LEU* 3.8 14.3 - - + +
447B MET* 4.1 20.6 - - - +
450B VAL* 3.5 8.5 - - - +
451B ALA* 3.4 27.5 - - - +
452B SER* 2.7 36.7 + - - -
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Residues in contact with LYS 439 (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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165B GLU* 3.2 23.6 + - - +
168B GLU* 3.5 33.0 + - - +
435B PHE* 2.8 36.9 + - + +
436B ARG* 2.9 22.1 + - - +
438B GLN* 1.3 71.7 - - - +
440B ALA* 1.3 60.8 + - - +
441B GLY 3.4 0.2 - - - -
442B PHE 3.1 18.9 + - - +
444B LEU* 3.9 13.8 - - + +
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Residues in contact with ALA 440 (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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47B GLU* 4.4 13.5 - - + +
50B MET* 3.5 21.5 - - + +
51B GLY* 4.4 11.3 - - - +
436B ARG 3.0 10.0 + - - +
437B ILE* 3.2 16.8 - - - +
438B GLN 3.1 0.8 - - - -
439B LYS* 1.3 79.3 - - - +
441B GLY* 1.3 55.5 + - - +
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Residues in contact with GLY 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B MET* 3.6 19.4 - - - +
56B ASP* 4.6 0.3 - - - +
59B LYS* 3.2 45.1 + - - +
437B ILE 3.7 2.0 + - - -
438B GLN 3.7 0.2 + - - -
440B ALA* 1.3 79.5 - - - +
442B PHE* 1.3 69.7 + - - +
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Residues in contact with PHE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B MET* 4.5 8.3 - - + -
56B ASP* 3.3 31.4 - - + -
59B LYS* 3.6 36.3 - - + -
60B ASP* 4.3 14.6 - - - -
63B TYR* 5.0 9.0 - + + -
438B GLN* 3.3 33.4 + - + +
439B LYS* 3.1 19.6 - - - +
440B ALA 3.7 0.6 - - - -
441B GLY* 1.3 87.2 - - - +
443B ASP* 1.3 59.8 + - - +
444B LEU* 3.3 16.7 + - + +
447B MET* 4.5 14.1 - - + -
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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
------------------------------------------------------------
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