Contacts of the helix formed by residues 13 - 32 (chain 4) 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 4).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113 PRO* 3.6 41.5 - - + +
123 ALA 3.5 15.0 - - - +
133 THR* 4.5 3.4 - - + -
114 PRO 4.1 8.7 - - - +
124 ALA* 1.3 79.8 - - - +
144 ALA* 1.3 64.8 + - - +
154 GLU* 3.2 18.6 + - - +
164 THR* 2.9 17.6 + - - +
174 GLN* 3.0 20.5 + - - +
434 PHE* 5.0 6.9 - - + -
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Residues in contact with ALA 14 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113 PRO* 5.6 0.4 - - - +
123 ALA 4.2 3.8 + - - -
393 LYS* 4.7 18.6 - - - +
134 THR* 1.3 72.9 - - - +
154 GLU* 1.3 66.6 + - - +
174 GLN* 3.3 9.2 + - - +
184 HIS* 2.9 23.9 + - - +
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Residues in contact with GLU 15 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113 PRO* 6.5 0.2 - - + -
134 THR* 3.2 10.7 + - - +
144 ALA* 1.3 80.3 - - - +
164 THR* 1.3 61.5 + - - +
184 HIS* 3.2 10.8 + - + +
194 ILE* 3.0 34.2 + - + +
534 TYR* 4.0 17.8 + - - -
714 GLN* 5.6 1.5 - - - +
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Residues in contact with THR 16 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124 ALA* 3.8 6.7 - - + -
134 THR* 2.9 30.1 + - - -
154 GLU* 1.3 77.1 - - - +
174 GLN* 1.3 64.6 + - - +
194 ILE* 3.2 12.7 + - + +
204 ALA* 3.0 21.7 + - - +
404 ALA* 3.9 6.7 - - + -
434 PHE* 3.4 45.6 - - + -
534 TYR* 6.2 0.7 - - + -
554 ILE* 3.8 23.9 - - + +
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Residues in contact with GLN 17 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124 ALA* 6.2 0.2 - - + -
134 THR 3.0 12.7 + - - +
144 ALA* 3.6 11.7 - - - +
154 GLU 3.2 0.2 - - - -
164 THR* 1.3 77.2 - - - +
184 HIS* 1.3 55.9 + - - +
204 ALA* 3.3 5.9 + - - +
214 ASP* 2.8 67.4 + - - +
384 PHE 2.9 21.1 + - - -
394 LYS* 3.6 8.8 - - - +
404 ALA* 2.9 33.7 + - + +
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Residues in contact with HIS 18 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144 ALA 2.9 16.9 + - - +
154 GLU* 3.4 12.8 - - + +
174 GLN* 1.3 72.0 - - - +
194 ILE* 1.3 67.7 + - + +
214 ASP* 3.2 8.6 + - - +
224 GLN* 2.9 67.8 + - + +
804 LEU* 4.8 6.5 - - + +
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Residues in contact with ILE 19 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154 GLU* 3.0 35.1 + - + +
164 THR* 3.2 10.3 + - - +
184 HIS* 1.3 84.9 - - + +
204 ALA* 1.3 64.5 + - - +
224 GLN* 3.2 9.9 + - - +
234 VAL* 3.5 13.0 + - - +
534 TYR* 3.7 43.5 - - + +
554 ILE* 3.7 17.5 - - + -
694 VAL* 3.7 27.1 - - + -
714 GLN* 4.6 7.9 - - - +
804 LEU* 4.1 22.9 - - + -
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Residues in contact with ALA 20 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164 THR 3.0 13.4 + - - +
174 GLN* 3.6 11.0 - - - +
194 ILE* 1.3 77.4 - - - +
214 ASP* 1.3 62.6 + - - +
234 VAL* 3.0 20.6 + - - +
244 ARG 3.1 9.5 + - - -
384 PHE* 3.3 26.5 - - + -
404 ALA* 4.4 15.7 - - + -
554 ILE* 4.2 5.3 - - + +
574 VAL* 4.4 5.2 - - + -
674 LEU* 4.4 11.4 - - + -
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Residues in contact with ASP 21 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174 GLN* 2.8 59.8 + - - +
184 HIS* 3.7 8.3 - - - +
204 ALA* 1.3 71.9 - - - +
224 GLN* 1.3 68.7 + - + +
234 VAL 3.2 0.9 + - - -
244 ARG* 3.3 22.7 + - - +
254 SER 4.8 0.7 + - - -
384 PHE* 4.2 8.9 - - - +
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Residues in contact with GLN 22 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184 HIS* 2.9 51.6 + - + +
194 ILE 3.7 5.8 - - - +
204 ALA 3.1 0.6 - - - -
214 ASP* 1.3 81.9 - - - +
234 VAL* 1.3 59.1 + - - +
244 ARG 3.5 0.2 - - - -
254 SER* 5.1 4.4 + - - -
264 GLN* 3.8 11.4 + - - -
804 LEU* 3.7 24.1 - - + +
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Residues in contact with VAL 23 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194 ILE 3.5 7.8 + - - +
204 ALA 3.0 14.6 + - - +
224 GLN* 1.3 82.1 - - - +
244 ARG* 1.3 66.5 + - - +
254 SER 3.3 3.1 - - - -
264 GLN* 3.0 32.6 + - - +
274 LEU* 3.1 11.5 + - + +
384 PHE* 5.4 0.2 - - + -
674 LEU* 3.9 17.3 - - + -
694 VAL* 3.8 40.6 - - + -
804 LEU* 3.9 15.5 - - + +
824 LEU* 4.0 20.4 - - + +
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Residues in contact with ARG 24 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204 ALA 3.1 5.0 + - - -
214 ASP* 3.3 19.4 + - - +
224 GLN 3.5 0.2 - - - -
234 VAL* 1.3 77.7 - - - +
254 SER* 1.3 58.7 + - - +
274 LEU* 3.1 4.2 + - - +
284 GLU* 2.8 50.8 + - + +
344 LYS* 3.8 18.8 - - - +
354 PHE* 3.0 33.9 + - + -
364 PRO* 4.0 9.5 + - - +
384 PHE* 3.7 45.0 - - + +
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Residues in contact with SER 25 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214 ASP 4.8 1.4 + - - -
224 GLN 5.1 3.8 + - - -
234 VAL 3.3 1.1 - - - -
244 ARG* 1.3 78.2 - - - +
264 GLN* 1.3 67.9 + - - +
284 GLU* 3.4 15.9 + - - +
294 GLU* 3.0 29.8 + - - +
789 LYS* 6.5 0.4 - - - -
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Residues in contact with GLN 26 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224 GLN 3.8 18.0 + - - -
234 VAL* 3.0 12.4 + - - +
254 SER* 1.3 82.5 + - - +
274 LEU* 1.3 63.7 + - - +
294 GLU* 3.4 6.4 + - - +
304 LYS* 3.1 28.3 + - + +
804 LEU 3.2 22.8 + - - -
814 THR* 3.6 7.2 - - - +
824 LEU* 2.9 41.0 + - + +
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Residues in contact with LEU 27 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234 VAL* 3.1 6.4 + - + +
244 ARG* 3.1 9.9 + - - +
264 GLN* 1.3 80.2 - - - +
284 GLU* 1.3 57.2 + - - +
304 LYS* 3.2 2.2 + - - -
314 GLU* 2.9 34.0 + - + +
354 PHE* 3.5 28.9 - - + -
384 PHE* 3.5 29.6 - - + -
654 VAL* 4.3 11.4 - - + -
674 LEU* 4.3 10.8 - - + -
824 LEU* 3.8 13.3 - - + +
854 TYR* 3.6 49.4 - - + -
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Residues in contact with GLU 28 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244 ARG* 2.8 37.2 + - + +
254 SER* 3.7 17.7 - - - +
264 GLN 3.3 0.4 - - - -
274 LEU* 1.3 76.2 - - - +
294 GLU* 1.3 53.1 + - - +
324 ASN* 2.8 30.0 + - - -
334 LYS 3.1 29.0 + - - +
344 LYS* 3.1 38.6 + - - +
354 PHE* 2.8 32.7 + - + -
799 PRO* 4.0 13.4 - - + +
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Residues in contact with GLU 29 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254 SER* 3.0 19.9 + - - +
264 GLN* 3.7 6.7 - - - +
284 GLU* 1.3 77.3 - - - +
304 LYS* 1.3 66.7 + - + +
324 ASN* 3.4 9.5 + - - +
769 GLU 5.1 1.8 - - - -
779 ASN* 3.6 49.7 + - + +
789 LYS* 4.5 19.4 - - + +
799 PRO* 4.7 2.5 - - + -
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Residues in contact with LYS 30 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264 GLN* 3.1 20.0 + - + +
274 LEU 3.8 2.5 - - - +
294 GLU* 1.3 81.6 - - + +
314 GLU* 1.3 61.0 + - - +
324 ASN* 3.6 0.9 + - - +
824 LEU* 5.4 2.5 - - + -
854 TYR* 3.4 32.4 + - + +
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Residues in contact with GLU 31 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274 LEU* 2.9 31.7 + - + +
284 GLU 4.3 0.4 - - - +
304 LYS* 1.3 77.5 - - - +
324 ASN* 1.3 70.6 + - - +
334 LYS* 3.3 27.3 + - + +
354 PHE* 4.2 12.4 - - + -
854 TYR* 2.7 34.5 + - + +
874 THR* 4.0 16.0 - - + +
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Residues in contact with ASN 32 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284 GLU 2.8 11.9 + - - -
294 GLU 3.4 7.2 + - - +
304 LYS 3.3 3.6 - - - +
314 GLU* 1.3 80.7 - - - +
334 LYS* 1.3 58.8 + - - +
229 GLN* 5.4 2.4 - - - +
779 ASN* 4.1 8.6 - - - +
789 LYS 4.2 2.3 - - - +
799 PRO* 3.4 25.7 - - - +
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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
------------------------------------------------------------
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