Contacts of the helix formed by residues 13 - 32 (chain 1) 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 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111 PRO 4.1 8.1 - - - +
121 ALA* 1.3 78.9 - - - +
141 ALA* 1.3 65.9 + - - +
151 GLU* 3.1 20.4 + - - +
161 THR* 2.9 23.5 + - - +
171 GLN* 3.0 12.5 + - - +
431 PHE* 4.7 8.9 - - + -
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Residues in contact with ALA 14 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730 LEU* 5.4 5.8 - - + -
750 HIS* 3.6 26.6 - - + +
131 THR* 1.3 75.3 - - - +
151 GLU* 1.3 57.0 + - - +
171 GLN* 3.2 8.8 + - - +
181 HIS* 2.8 28.8 + - - +
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Residues in contact with GLU 15 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730 LEU* 6.3 0.6 - - + +
740 PRO* 3.0 40.8 - - + +
750 HIS* 4.5 1.2 + - - -
131 THR* 3.1 11.4 + - - +
141 ALA* 1.3 76.9 - - - +
161 THR* 1.3 60.3 + - - +
181 HIS* 3.2 6.8 + - - +
191 ILE* 2.9 41.7 + - + +
531 TYR* 4.2 17.4 + - + -
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Residues in contact with THR 16 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121 ALA* 3.7 9.4 - - + -
131 THR* 2.9 31.2 + - - -
151 GLU* 1.3 77.4 - - - +
171 GLN* 1.3 62.2 + - - +
191 ILE* 3.2 9.2 + - - +
201 ALA* 2.9 22.7 + - - +
401 ALA* 3.8 6.5 - - + -
421 SER 4.5 0.2 - - - +
431 PHE* 3.4 36.3 - - + -
531 TYR* 6.3 0.7 - - + -
551 ILE* 3.8 32.3 - - + +
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Residues in contact with GLN 17 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121 ALA* 5.9 0.2 - - + -
131 THR 3.0 12.1 + - - +
141 ALA* 3.6 11.7 - - - +
161 THR* 1.3 76.7 - - - +
181 HIS* 1.3 56.9 + - - +
201 ALA* 3.4 4.5 + - - +
211 ASP* 2.9 63.3 + - - +
381 PHE 2.8 25.6 + - - -
391 LYS* 3.5 7.8 - - - +
401 ALA* 2.7 34.3 + - + +
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Residues in contact with HIS 18 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740 PRO* 3.8 36.9 + - + +
750 HIS* 4.1 24.3 - + + +
770 ASN* 6.1 0.2 - - - -
141 ALA 2.8 17.6 + - - +
151 GLU* 3.5 8.7 - - - +
171 GLN* 1.3 75.5 - - - +
191 ILE* 1.3 71.9 + - + +
211 ASP* 3.4 6.7 + - - +
221 GLN* 3.0 65.3 + - + +
801 LEU* 4.9 5.4 - - + +
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Residues in contact with ILE 19 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151 GLU* 2.9 36.4 + - + +
161 THR* 3.7 7.0 - - - +
181 HIS* 1.3 81.0 - - + +
201 ALA* 1.3 61.9 + - - +
221 GLN* 3.2 13.0 + - - +
231 VAL* 3.3 14.0 + - - +
531 TYR* 4.0 41.7 - - + +
551 ILE* 3.7 18.8 - - + -
691 VAL* 3.7 28.0 - - + -
711 GLN* 5.1 4.5 - - - +
801 LEU* 4.3 22.4 - - + -
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Residues in contact with ALA 20 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161 THR 2.9 16.1 + - - +
171 GLN* 3.8 7.0 - - - +
191 ILE* 1.3 75.1 - - - +
211 ASP* 1.3 63.6 + - - +
231 VAL* 3.1 11.5 + - - +
241 ARG 3.0 18.9 + - - -
381 PHE* 3.4 28.1 - - + -
401 ALA* 4.3 11.0 - - + -
551 ILE* 4.2 4.7 - - + +
571 VAL* 4.3 16.6 - - + -
671 LEU* 4.3 5.4 - - + -
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Residues in contact with ASP 21 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171 GLN* 2.9 53.4 + - - +
181 HIS* 3.7 7.6 - - - +
201 ALA* 1.3 75.5 - - - +
221 GLN* 1.3 70.3 + - - +
231 VAL 3.4 0.7 + - - -
241 ARG* 3.4 27.4 + - - +
251 SER 4.8 0.9 + - - -
381 PHE* 4.1 6.8 - - - +
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Residues in contact with GLN 22 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181 HIS* 3.0 62.4 + - - +
191 ILE 3.2 6.7 + - - +
211 ASP* 1.3 82.1 - - - +
231 VAL* 1.3 59.8 + - - +
251 SER* 4.8 5.9 + - - -
261 GLN* 3.8 10.6 + - - -
801 LEU* 3.7 26.6 - - + +
326 ASN 5.6 1.2 - - - +
336 LYS* 5.4 9.5 - - - +
346 LYS 5.8 1.6 + - - -
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Residues in contact with VAL 23 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191 ILE 3.3 10.9 + - - +
201 ALA 3.4 10.8 - - - +
221 GLN* 1.3 81.0 - - - +
241 ARG* 1.4 65.6 + - - +
251 SER 3.2 3.1 - - - -
261 GLN* 3.0 33.7 + - - +
271 LEU* 3.1 11.1 + - - +
381 PHE* 5.4 0.2 - - + -
671 LEU* 3.8 27.1 - - + -
691 VAL* 3.9 33.9 - - + -
801 LEU* 4.0 12.3 - - + +
821 LEU* 4.1 17.8 - - + +
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Residues in contact with ARG 24 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201 ALA 3.0 11.8 + - - +
211 ASP* 3.4 24.6 + - - +
231 VAL* 1.4 75.1 - - - +
251 SER* 1.3 59.0 + - - +
271 LEU* 3.2 4.2 + - - +
281 GLU* 2.9 57.2 + - + +
341 LYS* 5.9 0.6 - - - +
351 PHE* 2.7 30.1 + - - +
361 PRO 4.4 6.3 + - - -
371 VAL* 4.8 0.8 - - - +
381 PHE* 3.5 57.9 + - + +
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Residues in contact with SER 25 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
211 ASP 4.8 1.0 + - - -
221 GLN 4.8 5.8 + - - -
241 ARG* 1.3 79.2 - - - +
261 GLN* 1.3 59.6 + - - +
281 GLU* 3.7 16.6 - - - +
291 GLU* 2.9 31.9 + - - +
346 LYS 5.2 0.5 + - - -
366 PRO* 3.4 22.2 - - - +
376 VAL* 5.5 5.0 - - - +
616 ASP* 6.1 0.7 - - - -
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Residues in contact with GLN 26 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221 GLN 3.8 9.9 + - - -
231 VAL* 3.0 20.5 + - - +
251 SER* 1.3 78.5 + - - +
271 LEU* 1.3 64.1 + - - +
291 GLU* 3.9 1.9 - - - +
301 LYS* 3.0 28.4 + - + +
801 LEU 3.2 22.6 + - - -
811 THR* 3.6 4.3 - - - -
821 LEU* 2.8 41.7 + - + +
346 LYS* 3.5 25.4 - - + +
366 PRO* 3.8 27.9 - - + +
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Residues in contact with LEU 27 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231 VAL 3.1 9.2 + - - +
241 ARG* 3.2 9.2 + - - +
261 GLN* 1.3 77.0 - - - +
281 GLU* 1.3 51.8 + - - +
301 LYS* 3.1 5.0 + - - +
311 GLU* 2.8 38.7 + - + +
351 PHE* 3.5 29.4 - - + -
381 PHE* 3.6 24.2 - - + -
651 VAL* 4.0 19.3 - - + -
671 LEU* 4.1 4.9 - - + -
821 LEU* 3.7 12.4 - - + +
851 TYR* 3.5 49.1 - - + -
871 THR* 5.1 0.4 - - + -
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Residues in contact with GLU 28 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241 ARG* 2.9 48.9 + - - +
251 SER* 3.7 19.9 + - - +
271 LEU* 1.3 71.1 - - - +
291 GLU* 1.3 53.7 + - - +
311 GLU* 3.2 1.1 + - - +
321 ASN* 2.7 31.5 + - - -
331 LYS 3.1 27.7 + - - +
341 LYS* 3.7 30.6 + - + +
351 PHE* 3.7 30.0 + - + -
616 ASP* 5.7 0.2 - - - +
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Residues in contact with GLU 29 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251 SER 2.9 18.6 + - - +
261 GLN 3.9 2.9 - - - +
281 GLU* 1.3 74.7 - - - +
301 LYS* 1.3 64.0 + - - +
311 GLU 3.4 0.3 + - - -
321 ASN* 3.6 11.3 + - - +
366 PRO* 3.6 29.7 - - + +
376 VAL* 3.6 23.2 - - + +
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Residues in contact with LYS 30 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261 GLN* 3.0 19.8 + - + +
271 LEU 3.5 7.6 - - - +
291 GLU* 1.3 76.8 - - - +
311 GLU* 1.3 60.2 + - - +
321 ASN* 5.0 1.0 - - - +
821 LEU* 5.3 3.4 - - + -
851 TYR* 3.3 39.8 + - + +
632 ASP* 5.9 3.6 + - - -
882 ASN* 3.2 20.9 + - - +
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Residues in contact with GLU 31 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271 LEU* 2.8 32.9 + - + +
281 GLU 4.1 0.7 - - - +
301 LYS* 1.3 72.6 - - - +
321 ASN* 1.3 71.5 + - - +
331 LYS* 3.2 31.8 + - + +
351 PHE* 4.5 6.8 - - + -
851 TYR* 2.7 40.4 + - + +
871 THR* 3.8 18.2 + - + +
312 GLU* 4.3 13.2 - - - +
332 LYS* 3.7 22.3 + - - +
872 THR* 4.3 8.9 + - - -
882 ASN* 4.9 1.6 + - - +
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Residues in contact with ASN 32 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281 GLU 2.7 15.2 + - - -
291 GLU* 3.6 8.2 + - - +
301 LYS 3.4 3.1 - - - +
311 GLU* 1.3 76.7 - - - +
331 LYS* 1.3 58.9 + - - +
332 LYS* 5.1 7.4 + - - +
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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