Contacts of the helix formed by residues 13 - 32 (chain 2) 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 THR 13 (chain 2).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112 PRO 4.1 7.6 - - - +
122 ALA* 1.3 79.5 - - - +
142 ALA* 1.3 65.2 + - - +
152 GLU* 3.1 20.4 + - - +
162 THR* 2.9 24.9 + - - +
172 GLN* 3.1 12.4 + - - +
432 PHE* 4.8 8.3 - - + -
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Residues in contact with ALA 14 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132 THR* 1.3 75.6 - - - +
152 GLU* 1.3 56.9 + - - +
172 GLN* 3.3 9.6 + - - +
182 HIS* 2.9 28.3 + - - +
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Residues in contact with GLU 15 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132 THR* 3.1 11.2 + - - +
142 ALA* 1.3 77.0 - - - +
162 THR* 1.3 61.8 + - - +
182 HIS* 3.1 12.9 + - + +
192 ILE* 2.9 40.4 + - + +
532 TYR* 4.4 14.7 + - - -
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Residues in contact with THR 16 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122 ALA* 3.5 10.6 - - + -
132 THR* 2.9 29.8 + - - -
152 GLU* 1.3 78.6 - - - +
172 GLN* 1.3 60.7 + - - +
192 ILE* 3.2 11.0 + - - +
202 ALA* 3.0 23.0 + - - +
402 ALA* 3.9 6.5 - - + -
422 SER 4.6 0.2 - - - +
432 PHE* 3.5 33.0 - - + -
532 TYR* 6.2 0.7 - - + -
552 ILE* 3.7 31.5 - - + +
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Residues in contact with GLN 17 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132 THR 3.1 8.7 + - - +
142 ALA* 3.5 11.9 - - - +
162 THR* 1.3 78.0 - - - +
182 HIS* 1.3 58.2 + - - +
202 ALA* 3.4 5.7 + - - +
212 ASP* 2.8 65.5 + - - +
382 PHE 2.7 25.6 + - - -
392 LYS* 3.5 8.1 - - - +
402 ALA* 2.8 36.0 + - + +
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Residues in contact with HIS 18 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142 ALA 2.9 13.4 + - - +
152 GLU* 3.1 17.5 + - + +
172 GLN* 1.3 78.3 - - - +
192 ILE* 1.3 71.3 + - + +
212 ASP* 3.5 7.1 + - - -
222 GLN* 3.0 66.4 + - + +
802 LEU* 5.0 4.3 - - + +
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Residues in contact with ILE 19 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152 GLU* 2.9 35.8 + - + +
162 THR* 3.2 9.4 + - - +
182 HIS* 1.3 79.9 - - + +
202 ALA* 1.3 64.5 + - - +
222 GLN* 3.1 13.7 + - - +
232 VAL* 3.4 13.4 + - - +
532 TYR* 4.0 40.2 - - + +
552 ILE* 3.8 14.4 - - + -
692 VAL* 3.7 28.7 - - + -
712 GLN* 4.6 5.2 - - - +
802 LEU* 3.8 24.5 - - + -
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Residues in contact with ALA 20 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162 THR 3.0 15.7 + - - +
172 GLN* 3.6 10.3 - - - +
192 ILE* 1.3 76.5 - - - +
212 ASP* 1.3 61.2 - - - +
232 VAL* 3.1 20.3 + - - +
242 ARG 3.1 10.9 + - - -
382 PHE* 3.3 27.7 - - + -
402 ALA* 4.4 12.3 - - + -
552 ILE* 4.1 5.5 - - + +
572 VAL* 4.5 5.2 - - + -
672 LEU* 4.4 11.9 - - + -
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Residues in contact with ASP 21 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172 GLN* 2.8 58.4 + - - +
182 HIS* 3.7 7.5 - - - +
202 ALA* 1.3 72.6 - - - +
222 GLN* 1.3 70.7 + - - +
232 VAL 3.2 0.7 + - - -
242 ARG* 3.4 23.9 + - - +
252 SER 4.8 0.9 + - - -
382 PHE* 4.2 8.0 - - - +
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Residues in contact with GLN 22 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182 HIS* 3.0 62.6 + - - +
192 ILE 3.1 7.3 + - - +
212 ASP* 1.3 83.8 - - - +
232 VAL* 1.3 61.3 + - - +
252 SER* 4.9 5.6 + - - -
262 GLN* 3.9 9.2 + - - -
802 LEU* 3.6 30.6 - - + +
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Residues in contact with VAL 23 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192 ILE 3.4 8.9 + - - +
202 ALA* 3.1 14.0 + - - +
222 GLN* 1.3 80.8 - - - +
242 ARG* 1.3 65.9 + - - +
252 SER 3.2 3.4 - - - -
262 GLN* 3.0 32.0 + - - +
272 LEU* 3.1 11.3 + - + +
382 PHE* 5.4 0.2 - - + -
672 LEU* 3.9 24.9 - - + -
692 VAL* 3.9 34.1 - - + -
802 LEU* 4.0 10.5 - - + +
822 LEU* 4.0 23.7 - - + +
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Residues in contact with ARG 24 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202 ALA 3.1 6.2 + - - -
212 ASP* 3.4 21.6 + - - +
232 VAL* 1.3 75.5 - - - +
252 SER* 1.3 58.6 + - - +
272 LEU* 3.0 5.1 + - - +
282 GLU* 2.8 55.8 + - + +
342 LYS* 5.8 0.2 - - - +
352 PHE* 2.8 39.8 + - + +
362 PRO 4.6 1.2 + - - -
372 VAL* 4.3 4.2 - - - +
382 PHE* 3.4 61.9 + - + +
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Residues in contact with SER 25 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212 ASP 4.8 1.0 + - - -
222 GLN 4.9 5.2 + - - -
232 VAL 3.2 1.2 - - - -
242 ARG* 1.3 78.8 - - - +
262 GLN* 1.3 68.9 + - - +
282 GLU* 3.7 15.1 + - - +
292 GLU* 2.9 26.5 + - - +
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Residues in contact with GLN 26 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222 GLN 3.9 17.2 + - - -
232 VAL* 3.0 13.4 + - - +
252 SER* 1.3 84.2 + - - +
272 LEU* 1.3 62.5 + - - +
292 GLU* 3.4 6.2 + - - +
302 LYS* 3.0 29.0 + - + +
802 LEU 3.4 20.4 + - - -
812 THR* 3.6 6.2 - - - +
822 LEU* 2.8 42.7 + - + +
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Residues in contact with LEU 27 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232 VAL* 3.1 9.6 + - + +
242 ARG* 3.0 9.3 + - - +
262 GLN* 1.3 78.9 - - - +
282 GLU* 1.3 57.1 + - - +
302 LYS* 3.2 3.1 + - - -
312 GLU* 2.8 34.0 + - + +
352 PHE* 3.5 31.4 - - + -
382 PHE* 3.5 25.4 - - + -
652 VAL* 4.3 9.6 - - + -
672 LEU* 4.0 13.5 - - + -
822 LEU* 3.8 11.1 - - + +
852 TYR* 3.5 50.0 - - + -
872 THR* 5.3 0.4 - - + -
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Residues in contact with GLU 28 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242 ARG* 2.8 47.5 + - + +
252 SER* 3.7 18.5 + - - +
272 LEU* 1.3 72.1 - - - +
292 GLU* 1.3 52.4 + - - +
312 GLU* 4.8 0.4 - - - -
322 ASN* 2.8 30.0 + - - -
332 LYS 3.2 27.9 + - - +
342 LYS* 3.7 34.1 - - + +
352 PHE* 3.8 20.9 + - + -
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Residues in contact with GLU 29 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252 SER 2.9 16.4 + - - +
262 GLN* 3.6 7.0 - - - +
282 GLU* 1.3 74.2 - - - +
302 LYS* 1.3 67.3 + - + +
322 ASN* 3.2 14.1 + - - +
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Residues in contact with LYS 30 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631 ASP* 5.6 4.4 - - - +
881 ASN* 2.9 32.9 + - - +
262 GLN* 3.0 20.2 + - + +
272 LEU 3.9 1.8 - - - +
292 GLU* 1.3 78.4 - - + +
312 GLU* 1.3 59.2 + - - +
322 ASN* 3.7 0.7 + - - +
822 LEU* 5.5 5.2 - - + +
842 ASN* 6.3 0.8 - - - +
852 TYR* 3.4 30.9 + - + +
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Residues in contact with GLU 31 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311 GLU* 4.3 13.7 - - - +
331 LYS* 4.0 20.0 + - - +
871 THR* 4.5 7.9 + - - -
881 ASN* 5.0 1.6 + - - +
272 LEU* 2.8 31.4 + - + +
282 GLU 4.2 0.9 - - - +
302 LYS* 1.3 73.5 - - - +
322 ASN* 1.3 70.9 + - - +
332 LYS* 3.3 32.8 + - + +
352 PHE* 4.5 10.4 - - + -
852 TYR* 2.6 41.6 + - + +
872 THR* 3.9 16.4 + - + +
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Residues in contact with ASN 32 (chain 2).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331 LYS* 5.2 9.1 - - - +
282 GLU 2.8 11.2 + - - -
292 GLU* 3.2 11.3 + - - +
302 LYS 3.4 1.1 - - - +
312 GLU* 1.3 81.6 - - - +
332 LYS* 1.3 59.5 + - - +
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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