Contacts of the helix formed by residues 34 - 47 (chain 0) in PDB entry 5JPQ
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 34 (chain 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320 THR 3.8 0.6 + - - -
330 ALA* 1.3 68.2 - - - +
350 LYS* 1.3 63.7 + - - -
360 GLU* 4.2 4.4 - - - +
370 LYS* 2.7 38.0 + - - +
380 ILE* 3.0 9.9 + - - +
5192 C 2.9 31.6 + - - -
5202 A 2.2 31.2 - - - -
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Residues in contact with LYS 35 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340 SER 1.3 63.9 - - - +
360 GLU* 1.3 62.8 + - + +
380 ILE* 3.1 8.7 + - - +
390 ARG* 2.8 25.2 + - - +
550 VAL* 4.0 35.3 - - + +
560 TYR* 5.2 0.2 - - - -
580 PHE* 4.7 4.5 - - + -
910 LYS* 4.0 22.2 - - - +
5202 A 1.5 73.6 + - - +
5212 A 0.6 136.3 + - - +
5262 A 4.9 0.4 + - - -
5282 U 3.6 11.0 + - - +
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Residues in contact with GLU 36 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340 SER* 2.8 8.9 + - - +
350 LYS* 1.3 78.3 - - - +
370 LYS* 1.3 63.4 + - - +
390 ARG* 2.9 30.2 + - - +
400 GLU* 3.5 17.7 + - - +
930 LYS* 4.6 13.2 + - - -
5202 A 3.7 15.5 + - - +
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Residues in contact with LYS 37 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20 THR* 3.0 35.2 - - - +
30 ILE* 3.4 19.5 - - + +
330 ALA* 5.7 3.4 - - + -
340 SER* 2.7 26.3 + - - +
360 GLU* 1.3 75.8 - - - +
380 ILE* 1.3 61.3 + - + +
400 GLU* 3.4 8.7 + - - +
410 GLU* 3.3 25.5 + - + +
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Residues in contact with ILE 38 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30 ILE* 6.4 0.2 - - + -
50 ILE* 3.7 24.7 - - + +
230 LEU* 5.1 6.1 - - + -
250 VAL* 3.9 13.0 - - + -
320 THR* 5.9 0.2 - - + -
330 ALA* 3.2 46.4 - - + +
340 SER 3.0 6.7 + - - +
350 LYS* 3.5 6.5 - - - +
370 LYS* 1.3 76.3 - - - +
390 ARG* 1.3 63.2 + - - +
410 GLU* 3.6 0.6 + - - -
420 LEU* 3.2 24.5 + - + +
550 VAL* 5.1 7.4 - - + -
580 PHE* 3.6 37.5 - - + -
670 SER* 6.1 0.2 - - - -
5202 A 4.0 7.6 - - - +
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Residues in contact with ARG 39 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350 LYS 2.8 13.0 + - - +
360 GLU* 3.0 23.2 - - - +
380 ILE* 1.3 78.6 - - - +
400 GLU* 1.3 59.3 + - + +
420 LEU* 3.7 5.0 - - - +
430 ALA* 3.1 25.2 + - - +
500 ALA* 3.4 21.8 + - + +
510 ARG* 3.6 30.8 + - - +
530 VAL* 2.9 35.7 + - + +
540 VAL* 4.1 15.7 - - - +
550 VAL* 5.0 13.6 - - + +
920 VAL* 4.3 31.1 - - - +
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Residues in contact with GLU 40 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360 GLU* 3.5 21.3 + - - +
370 LYS* 3.4 9.0 + - - +
380 ILE 3.2 0.2 - - - -
390 ARG* 1.3 80.7 - - + +
410 GLU* 1.3 65.8 + - - +
420 LEU 2.9 1.6 - - - -
430 ALA* 3.8 5.6 - - + +
440 LYS* 3.1 37.0 + - + +
500 ALA* 4.3 18.8 - - + +
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Residues in contact with GLU 41 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20 THR* 4.2 12.0 - - - +
30 ILE* 3.1 50.9 - - - +
40 VAL* 3.8 0.6 + - - -
50 ILE* 3.4 22.2 + - + +
370 LYS* 3.3 17.8 + - + +
380 ILE* 3.6 0.6 + - - -
400 GLU* 1.3 78.2 - - - +
420 LEU* 1.3 59.2 + - - +
440 LYS* 3.8 11.9 + - + +
450 GLN* 3.5 33.5 + - + +
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Residues in contact with LEU 42 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50 ILE* 4.4 14.3 - - + +
70 THR* 5.4 5.4 - - - -
210 LEU* 3.9 11.9 - - + -
230 LEU* 3.7 26.9 - - + -
380 ILE* 3.2 19.3 + - + +
390 ARG* 3.7 2.7 - - - +
400 GLU 2.9 0.6 - - - -
410 GLU* 1.3 75.4 - - - +
430 ALA* 1.3 64.2 + - - +
440 LYS 3.0 1.3 - - - -
450 GLN* 2.9 22.3 + - + +
460 LEU* 3.0 31.0 + - + +
530 VAL* 3.3 31.9 - - + -
550 VAL* 5.7 2.0 - - + -
710 ALA* 4.3 19.1 - - + -
730 VAL* 5.4 1.1 - - + -
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Residues in contact with ALA 43 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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390 ARG 3.1 16.0 + - - +
400 GLU* 3.3 7.6 + - + +
420 LEU* 1.3 81.5 - - - +
440 LYS* 1.3 54.0 + - + +
460 LEU* 4.6 4.3 - - - -
470 LYS* 2.5 29.6 + - - -
480 VAL 2.8 33.4 + - - +
490 ASP 4.4 0.7 - - - +
500 ALA* 4.0 18.6 - - + +
530 VAL* 4.8 9.2 - - + -
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Residues in contact with LYS 44 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400 GLU* 3.1 29.0 + - + +
410 GLU* 3.8 10.8 - - + +
420 LEU 3.0 1.0 - - - -
430 ALA* 1.3 75.9 - - + +
450 GLN* 1.3 65.8 + - + +
470 LYS* 3.2 24.0 + - - +
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Residues in contact with GLN 45 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50 ILE* 3.6 45.5 + - - +
70 THR* 5.3 9.5 + - - +
410 GLU* 3.5 24.9 + - + +
420 LEU* 2.9 13.2 + - + +
440 LYS* 1.3 79.0 - - + +
460 LEU* 1.3 64.4 + - + +
470 LYS* 4.2 9.7 - - - +
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Residues in contact with LEU 46 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70 THR* 6.3 4.7 - - + -
100 ILE* 6.1 4.9 - - + -
190 ARG* 3.9 25.2 + - - +
210 LEU* 4.9 8.3 - - + -
420 LEU* 3.0 40.4 + - + +
430 ALA 4.0 2.0 - - - +
450 GLN* 1.3 80.6 - - + +
470 LYS* 1.3 75.5 + - - +
480 VAL* 3.6 16.9 - - + +
530 VAL* 4.6 4.3 - - + -
730 VAL* 3.5 32.5 - - + -
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Residues in contact with LYS 47 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430 ALA 2.5 16.4 + - - -
440 LYS* 3.2 18.1 + - - +
450 GLN* 4.6 7.4 - - - +
460 LEU* 1.3 81.2 - - - +
480 VAL* 1.3 59.0 + - - +
1490 LYS* 5.4 7.7 + - - +
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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