Contacts of the helix formed by residues 13 - 32 (chain 8) 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 8).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118 PRO 4.1 8.1 - - - +
128 ALA* 1.3 79.1 - - - +
148 ALA* 1.3 65.5 + - - +
158 GLU* 3.2 18.9 + - - +
168 THR* 2.9 25.3 + - - +
178 GLN* 3.1 12.1 + - - +
438 PHE* 4.7 9.0 - - + -
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Residues in contact with ALA 14 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138 THR* 1.3 75.2 - - - +
158 GLU* 1.3 57.3 + - - +
178 GLN* 3.2 10.0 + - - +
188 HIS* 2.9 29.2 + - - +
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Residues in contact with GLU 15 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138 THR* 3.1 10.6 + - - +
148 ALA* 1.3 78.7 - - - +
168 THR* 1.3 56.6 + - - +
188 HIS* 3.1 12.3 + - + +
198 ILE* 2.9 45.6 + - + +
538 TYR* 4.6 12.5 + - - -
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Residues in contact with THR 16 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128 ALA* 3.7 13.7 - - + -
138 THR* 2.9 31.3 + - - -
158 GLU* 1.3 77.9 - - - +
178 GLN* 1.3 61.4 + - - +
198 ILE* 3.2 10.5 + - + +
208 ALA* 3.0 23.0 + - - +
408 ALA* 3.9 1.1 - - + -
428 SER 4.6 0.2 - - - +
438 PHE* 3.4 43.3 - - + -
538 TYR* 6.2 0.7 - - + -
558 ILE* 3.7 24.2 - - + +
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Residues in contact with GLN 17 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138 THR 3.1 11.6 + - - +
148 ALA* 3.5 12.3 - - + +
168 THR* 1.3 75.7 - - - +
188 HIS* 1.3 57.5 - - - +
208 ALA* 3.4 6.5 + - - +
218 ASP* 2.8 63.9 + - - +
388 PHE* 2.8 25.8 + - - -
398 LYS* 3.5 7.8 - - - +
408 ALA* 2.7 34.7 + - + +
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Residues in contact with HIS 18 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148 ALA 2.9 13.3 + - - +
158 GLU* 3.1 16.6 + - + +
178 GLN* 1.3 77.9 - - - +
198 ILE* 1.3 70.0 + - + +
218 ASP* 3.4 8.7 + - - +
228 GLN* 3.0 61.2 + - + +
808 LEU* 5.0 4.5 - - + +
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Residues in contact with ILE 19 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158 GLU* 2.9 35.5 + - + +
168 THR* 3.7 9.9 - - - +
188 HIS* 1.3 78.8 - - + +
208 ALA* 1.3 64.6 + - - +
228 GLN* 3.2 13.5 + - - +
238 VAL* 3.4 13.6 + - - +
538 TYR* 3.9 42.2 - - + +
558 ILE* 3.8 16.6 - - + -
698 VAL* 3.8 26.0 - - + -
718 GLN* 4.8 6.3 - - - +
808 LEU* 4.0 22.7 - - + -
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Residues in contact with ALA 20 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168 THR 3.0 17.0 + - - +
178 GLN* 3.6 9.6 - - - +
198 ILE* 1.3 74.4 - - - +
218 ASP* 1.3 65.3 + - - +
238 VAL* 3.0 19.6 + - - +
248 ARG 3.1 9.9 + - - -
388 PHE* 3.4 26.3 - - + -
408 ALA* 4.5 11.9 - - + -
558 ILE* 4.1 5.5 - - + +
578 VAL* 4.5 5.8 - - + -
678 LEU* 4.4 11.0 - - + -
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Residues in contact with ASP 21 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
178 GLN* 2.8 54.8 + - - +
188 HIS* 3.7 7.9 - - - +
208 ALA* 1.3 72.4 - - - +
228 GLN* 1.3 68.7 + - - +
238 VAL 3.3 0.7 + - - -
248 ARG* 3.3 27.0 + - - +
258 SER 4.8 0.9 + - - -
388 PHE* 4.3 7.4 - - - +
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Residues in contact with GLN 22 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188 HIS* 3.0 48.9 + - - +
198 ILE 3.5 8.5 - - - +
208 ALA 3.2 0.2 - - - -
218 ASP* 1.3 81.5 - - - +
238 VAL* 1.3 60.3 + - - +
248 ARG 3.6 0.2 - - - -
258 SER* 5.0 5.5 + - - -
268 GLN* 4.0 8.3 + - - -
808 LEU* 3.7 28.6 - - + +
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Residues in contact with VAL 23 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198 ILE 3.4 9.6 + - - +
208 ALA 3.0 14.6 + - - +
228 GLN* 1.3 80.6 - - - +
248 ARG* 1.3 63.3 + - - +
258 SER 3.2 3.4 - - - -
268 GLN* 3.1 31.8 + - - +
278 LEU* 3.1 12.2 + - + +
678 LEU* 3.8 25.1 - - + -
698 VAL* 3.8 33.9 - - + -
808 LEU* 4.1 9.9 - - + +
828 LEU* 3.9 24.4 - - + +
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Residues in contact with ARG 24 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208 ALA 3.1 5.8 + - - +
218 ASP* 3.3 23.4 + - - +
238 VAL* 1.3 76.8 - - - +
258 SER* 1.3 57.1 - - - +
278 LEU* 3.5 2.8 + - - +
288 GLU* 2.9 58.7 + - + +
348 LYS* 5.9 0.6 - - - +
358 PHE* 3.0 30.5 + - - +
368 PRO 4.7 0.6 + - - -
378 VAL* 4.2 5.7 - - - +
388 PHE* 3.4 64.3 + - + +
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Residues in contact with SER 25 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218 ASP 4.8 1.0 + - - -
228 GLN 5.0 5.1 + - - -
238 VAL 5.0 0.9 - - - -
248 ARG* 1.3 76.7 - - - +
268 GLN* 1.3 65.8 + - - +
288 GLU* 3.7 13.0 - - - +
298 GLU* 2.9 31.0 + - - +
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Residues in contact with GLN 26 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228 GLN 4.0 9.5 + - - -
238 VAL* 3.1 19.1 + - - +
258 SER* 1.3 82.6 + - - +
278 LEU* 1.3 58.0 + - - +
298 GLU* 3.4 8.0 + - - +
308 LYS* 3.0 33.5 + - + +
808 LEU 3.3 23.4 + - - -
818 THR* 3.7 5.7 - - - +
828 LEU* 2.8 41.6 + - + +
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Residues in contact with LEU 27 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238 VAL 3.1 12.0 + - - +
248 ARG* 3.7 8.3 - - - +
268 GLN* 1.3 77.2 - - - +
288 GLU* 1.3 57.7 + - - +
308 LYS* 3.1 3.4 + - - +
318 GLU* 2.8 33.8 + - + +
358 PHE* 3.4 31.4 - - + -
388 PHE* 3.5 24.9 - - + -
658 VAL* 4.3 11.4 - - + -
678 LEU* 4.1 12.1 - - + -
828 LEU* 3.8 11.1 - - + +
858 TYR* 3.5 50.0 - - + -
878 THR* 5.3 0.2 - - + -
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Residues in contact with GLU 28 (chain 8).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248 ARG* 2.9 52.4 + - - +
258 SER* 3.3 13.9 + - - +
278 LEU* 1.3 75.3 - - - +
298 GLU* 1.3 56.3 + - - +
318 GLU* 4.7 0.4 - - - -
328 ASN* 3.0 24.9 + - - -
338 LYS 3.2 29.5 + - - +
348 LYS* 3.5 31.0 - - + +
358 PHE* 3.6 27.6 + - + -
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Residues in contact with GLU 29 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258 SER 2.9 17.7 + - - +
268 GLN* 3.4 8.3 - - - +
288 GLU* 1.3 76.1 - - - +
308 LYS* 1.3 71.3 + - - +
328 ASN* 3.3 14.0 + - - +
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Residues in contact with LYS 30 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268 GLN* 3.0 22.0 + - + +
278 LEU 3.1 2.2 + - - +
298 GLU* 1.3 86.6 - - - +
318 GLU* 1.3 59.7 + - - +
328 ASN* 3.8 0.3 + - - +
828 LEU* 5.4 6.1 - - + +
848 ASN* 6.2 0.8 - - - +
858 TYR* 3.5 32.8 + - + +
639 ASP* 5.6 3.0 - - - +
889 ASN* 3.0 30.9 + - - +
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Residues in contact with GLU 31 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278 LEU* 2.8 27.9 + - + +
288 GLU 4.2 1.3 - - - +
308 LYS* 1.3 76.5 - - - +
328 ASN* 1.3 70.5 + - - +
338 LYS* 3.3 33.7 + - + +
358 PHE* 4.4 9.1 - - + -
858 TYR* 2.6 41.3 + - + +
878 THR* 3.8 16.3 + - + +
319 GLU* 4.3 13.3 - - - +
339 LYS* 4.2 16.4 + - - +
879 THR* 4.3 8.1 + - - -
889 ASN* 4.9 1.4 + - - +
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Residues in contact with ASN 32 (chain 8).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288 GLU 3.0 8.8 + - - -
298 GLU* 3.3 10.3 + - - +
308 LYS 3.5 0.8 - - - +
318 GLU* 1.3 79.3 - - - +
338 LYS* 1.3 61.1 + - - +
339 LYS* 5.0 10.9 - - - +
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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