Contacts of the helix formed by residues 23 - 32 (chain 0) in PDB entry 4N6V
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 VAL 23 (chain 0).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190 ILE 3.7 6.5 + - - +
200 ALA 3.8 9.9 - - - +
220 GLN* 1.3 77.7 - - - +
240 ARG* 1.3 67.0 + - - +
250 SER 3.4 2.2 - - - -
260 GLN* 3.3 26.1 + - - +
270 LEU* 3.1 18.5 + - + +
380 PHE* 5.5 0.4 - - + -
670 LEU* 4.2 15.5 - - + -
690 VAL* 4.0 33.4 - - + -
800 LEU* 4.3 12.6 - - + +
820 LEU* 4.0 33.5 - - + +
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Residues in contact with ARG 24 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200 ALA 3.4 4.9 + - - +
210 ASP* 3.2 20.9 + - - +
220 GLN 3.4 0.2 - - - -
230 VAL* 1.3 73.7 - - - +
250 SER* 1.3 71.3 + - - +
270 LEU* 2.9 6.4 + - - +
280 GLU* 2.2 60.6 + - + +
340 LYS* 4.4 10.9 - - - +
350 PHE* 3.4 28.5 + - - +
360 PRO 5.4 0.6 - - - -
370 VAL* 4.8 1.4 - - - +
380 PHE* 3.2 62.8 - - + +
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Residues in contact with SER 25 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210 ASP 4.7 0.6 + - - -
220 GLN 5.0 1.5 + - - -
240 ARG* 1.3 75.3 - - - +
260 GLN* 1.3 65.6 + - - +
280 GLU* 2.5 42.5 + - - +
290 GLU* 2.9 23.3 + - - +
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Residues in contact with GLN 26 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220 GLN 2.7 28.9 + - - -
230 VAL* 3.3 28.0 - - - +
240 ARG 3.3 0.4 - - - -
250 SER* 1.3 84.6 - - - +
270 LEU* 1.3 50.3 + - - +
290 GLU* 3.8 13.2 + - - +
300 LYS* 2.4 40.8 + - + +
800 LEU 3.8 12.5 + - - +
810 THR* 4.9 0.5 - - - -
820 LEU* 4.3 20.3 + - + +
345 LYS* 3.7 44.7 - - + +
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Residues in contact with LEU 27 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230 VAL 3.1 10.7 + - - +
240 ARG* 2.9 9.9 + - - +
250 SER 2.8 4.0 + - - -
260 GLN* 1.3 73.4 - - - +
280 GLU* 1.3 58.3 + - - +
290 GLU 3.3 0.2 - - - -
300 LYS* 3.3 6.0 - - - +
310 GLU* 3.0 28.8 + - + +
350 PHE* 3.6 27.8 - - + -
380 PHE* 3.9 26.7 - - + -
650 VAL* 4.6 10.5 - - + -
670 LEU* 4.4 13.9 - - + -
820 LEU* 4.1 6.9 - - + +
850 TYR* 3.4 55.9 - - + -
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Residues in contact with GLU 28 (chain 0).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240 ARG* 2.2 61.0 + - + +
250 SER* 2.5 30.0 + - - +
270 LEU* 1.3 70.4 - - - +
290 GLU* 1.3 61.9 + - + +
320 ASN* 3.0 24.1 + - - -
330 LYS 3.1 29.0 + - - +
340 LYS* 3.6 37.1 + - + +
350 PHE* 3.7 10.7 + - + +
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Residues in contact with GLU 29 (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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250 SER* 2.9 23.0 + - - +
260 GLN* 4.1 16.0 + - - +
280 GLU* 1.3 76.4 - - + +
300 LYS* 1.3 69.4 + - - +
320 ASN* 3.2 11.6 + - - +
285 GLU 5.9 0.2 - - - -
295 GLU* 3.2 44.7 + - - +
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Residues in contact with LYS 30 (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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260 GLN* 2.4 36.1 - - + +
270 LEU* 3.3 9.9 - - - +
290 GLU* 1.3 81.6 - - - +
310 GLU* 1.3 61.3 + - - +
320 ASN* 3.4 1.4 + - - +
820 LEU* 4.5 7.9 - - + -
850 TYR* 3.1 35.5 + - + +
325 ASN* 5.7 4.9 - - - -
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Residues in contact with GLU 31 (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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270 LEU* 3.0 18.0 + - + +
290 GLU 3.3 0.2 - - - -
300 LYS* 1.3 77.9 - - - +
320 ASN* 1.3 64.2 + - - +
330 LYS* 2.7 46.2 - - + +
350 PHE* 4.4 13.6 - - + -
850 TYR* 2.3 45.8 + - + +
870 THR* 3.9 15.0 - - + +
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Residues in contact with ASN 32 (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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280 GLU 3.0 8.2 + - - -
290 GLU* 3.2 10.4 + - - +
300 LYS 3.3 1.7 - - - +
310 GLU* 1.3 80.5 - - - +
330 LYS* 1.3 59.0 + - - +
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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