Contacts of the helix formed by residues 13 - 32 (chain 6) 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 6).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116 PRO 4.0 8.5 - - - +
126 ALA* 1.3 81.3 - - - +
146 ALA* 1.3 64.4 + - - +
156 GLU* 3.2 18.8 + - - +
166 THR* 2.9 14.9 + - - +
176 GLN* 3.0 21.2 + - - +
436 PHE* 4.9 7.1 - - + -
117 PRO* 3.7 39.7 - - + +
127 ALA 3.4 16.4 - - - +
137 THR* 4.6 3.1 - - + -
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Residues in contact with ALA 14 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136 THR* 1.3 74.7 - - - +
156 GLU* 1.3 58.0 + - - +
176 GLN* 3.3 8.5 + - - +
186 HIS* 2.9 29.7 + - - +
117 PRO* 5.7 0.4 - - - +
127 ALA 4.2 4.0 + - - -
397 LYS* 4.9 16.8 - - - +
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Residues in contact with GLU 15 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136 THR* 3.2 10.2 + - - +
146 ALA* 1.3 78.8 - - - +
166 THR* 1.3 62.4 + - - +
186 HIS* 3.2 11.1 + - + +
196 ILE* 3.0 36.1 + - + +
536 TYR* 3.8 20.7 + - - -
716 GLN* 5.9 2.2 - - - +
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Residues in contact with THR 16 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126 ALA* 3.7 13.9 - - + -
136 THR* 2.9 30.5 + - - -
156 GLU* 1.3 76.9 - - - +
176 GLN* 1.3 64.1 + - - +
196 ILE* 3.2 12.2 + - + +
206 ALA* 2.9 22.7 + - - +
406 ALA* 3.9 1.8 - - + -
426 SER 4.5 0.2 - - - +
436 PHE* 3.4 44.3 - - + -
536 TYR* 6.2 0.4 - - + -
556 ILE* 3.8 23.8 - - + +
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Residues in contact with GLN 17 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126 ALA* 6.1 0.2 - - + -
136 THR 3.0 11.5 + - - +
146 ALA* 3.6 11.2 - - - +
156 GLU 3.2 0.2 - - - -
166 THR* 1.3 79.0 - - - +
186 HIS* 1.3 56.8 + - - +
206 ALA* 3.3 4.5 + - - +
216 ASP* 2.8 66.7 + - - +
386 PHE 2.9 21.6 + - - -
396 LYS* 3.6 8.6 - - - +
406 ALA* 2.8 35.1 + - + +
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Residues in contact with HIS 18 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146 ALA 2.9 17.7 + - - +
156 GLU* 3.4 12.1 - - + +
176 GLN* 1.3 74.6 - - - +
196 ILE* 1.3 65.5 + - + +
216 ASP* 3.2 8.7 + - - +
226 GLN* 2.9 65.6 + - + +
806 LEU* 5.0 5.5 - - + +
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Residues in contact with ILE 19 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156 GLU* 3.0 36.3 + - + +
166 THR* 3.6 10.1 - - - +
186 HIS* 1.3 79.5 - - + +
206 ALA* 1.3 62.4 + - - +
226 GLN* 3.2 12.0 + - - +
236 VAL* 3.4 13.0 + - - +
536 TYR* 3.7 44.6 - - + +
556 ILE* 3.7 16.8 - - + -
696 VAL* 3.8 26.2 - - + -
716 GLN* 4.6 7.6 - - - +
806 LEU* 4.2 20.8 - - + +
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Residues in contact with ALA 20 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166 THR 2.9 16.3 + - - +
176 GLN* 3.6 7.6 - - - +
196 ILE* 1.3 76.5 - - - +
216 ASP* 1.3 63.7 + - - +
236 VAL* 3.0 20.8 + - - +
246 ARG 3.1 10.4 + - - -
386 PHE* 3.3 26.5 - - + -
406 ALA* 4.4 15.3 - - + -
556 ILE* 4.1 6.3 - - + +
576 VAL* 4.4 4.3 - - + -
676 LEU* 4.4 11.9 - - + -
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Residues in contact with ASP 21 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176 GLN* 2.8 55.4 + - - +
186 HIS* 3.2 8.2 + - - +
206 ALA* 1.3 73.4 - - - +
226 GLN* 1.3 67.1 + - + +
236 VAL 3.2 1.2 + - - -
246 ARG* 3.3 24.6 + - - +
256 SER 4.8 0.9 + - - -
386 PHE* 4.2 9.5 - - - +
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Residues in contact with GLN 22 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186 HIS* 2.9 48.5 + - + +
196 ILE 3.6 5.6 - - - +
206 ALA 3.1 0.6 - - - -
216 ASP* 1.3 79.8 - - - +
236 VAL* 1.3 59.4 + - - +
246 ARG 3.5 0.4 - - - -
256 SER* 5.1 4.6 + - - -
266 GLN* 3.8 10.7 + - - -
796 PRO* 6.0 1.6 - - - +
806 LEU* 3.7 27.4 + - + +
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Residues in contact with VAL 23 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196 ILE 3.4 7.8 + - - +
206 ALA 3.0 13.8 + - - +
226 GLN* 1.3 78.4 - - - +
246 ARG* 1.3 66.0 + - - +
256 SER 3.3 2.5 - - - -
266 GLN* 3.0 33.3 + - - +
276 LEU* 3.2 11.7 + - + +
386 PHE* 5.3 0.2 - - + -
676 LEU* 3.9 17.3 - - + -
696 VAL* 3.8 41.5 - - + -
806 LEU* 3.9 14.6 - - + +
826 LEU* 3.9 21.0 - - + +
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Residues in contact with ARG 24 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206 ALA 3.1 5.6 + - - +
216 ASP* 3.3 20.1 + - - +
226 GLN 3.5 0.2 - - - -
236 VAL* 1.3 76.9 - - - +
256 SER* 1.3 58.8 + - - +
276 LEU* 3.0 4.9 + - - +
286 GLU* 2.6 69.0 + - + +
346 LYS* 3.6 20.0 - - - +
356 PHE* 3.4 27.6 + - + -
366 PRO* 4.6 3.8 - - - +
386 PHE* 3.7 44.0 - - + -
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Residues in contact with SER 25 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216 ASP 4.8 0.8 + - - -
226 GLN 5.1 4.6 + - - -
236 VAL 3.3 1.3 - - - -
246 ARG* 1.3 80.2 - - - +
266 GLN* 1.3 66.3 + - - +
286 GLU* 3.7 16.9 + - - +
296 GLU* 3.0 41.0 + - - +
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Residues in contact with GLN 26 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226 GLN 3.8 17.6 + - - -
236 VAL* 3.0 12.2 + - - +
256 SER* 1.3 79.8 + - - +
276 LEU* 1.3 64.7 + - - +
296 GLU* 3.4 6.4 + - - +
306 LYS* 3.1 28.8 + - + +
806 LEU 3.2 22.0 + - - -
816 THR* 3.6 7.3 - - - +
826 LEU* 2.9 41.0 + - + +
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Residues in contact with LEU 27 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236 VAL 3.2 6.2 + - - +
246 ARG* 3.0 9.5 + - - +
266 GLN* 1.3 81.5 - - - +
286 GLU* 1.3 56.8 + - - +
306 LYS* 3.3 2.9 + - - +
316 GLU* 2.9 33.4 + - + +
356 PHE* 3.5 24.2 - - + -
386 PHE* 3.5 32.5 - - + -
656 VAL* 4.3 12.8 - - + -
676 LEU* 4.2 9.9 - - + -
826 LEU* 3.8 14.3 - - + +
856 TYR* 3.6 49.4 - - + -
876 THR* 5.5 0.2 - - + -
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Residues in contact with GLU 28 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791 PRO* 4.0 12.8 - - + +
246 ARG* 2.6 60.1 + - + +
256 SER* 3.7 18.4 - - - +
266 GLN 3.3 0.2 - - - -
276 LEU* 1.3 73.1 - - - +
296 GLU* 1.3 58.3 + - + +
326 ASN* 2.9 25.6 + - - -
336 LYS 3.2 28.6 + - - +
346 LYS* 3.3 27.0 + - - +
356 PHE* 2.8 27.7 + - + -
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Residues in contact with GLU 29 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
771 ASN* 3.2 48.9 - - + +
781 LYS* 3.3 35.3 + - + +
791 PRO* 4.7 3.1 - - + -
256 SER* 3.0 25.5 + - - +
266 GLN* 4.0 5.6 - - - +
276 LEU 3.2 0.2 - - - -
286 GLU* 1.3 78.4 - - + +
306 LYS* 1.3 63.4 + - + +
326 ASN* 3.4 10.6 + - - +
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Residues in contact with LYS 30 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145 ALA* 6.2 1.8 - - + -
185 HIS* 5.5 7.3 + - - -
266 GLN* 3.1 19.4 + - + +
276 LEU 3.8 2.7 - - - +
296 GLU* 1.3 78.4 - - - +
316 GLU* 1.3 61.6 + - - +
326 ASN* 3.5 1.6 + - - +
826 LEU* 5.3 2.9 - - + -
856 TYR* 3.4 34.2 + - + +
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Residues in contact with GLU 31 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276 LEU* 2.9 25.6 + - + +
306 LYS* 1.3 76.0 - - - +
326 ASN* 1.3 70.4 + - - +
336 LYS* 3.2 28.6 + - + +
356 PHE* 4.1 11.7 - - + -
856 TYR* 2.7 41.2 + - + +
876 THR* 4.0 14.3 - - + +
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Residues in contact with ASN 32 (chain 6).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221 GLN* 5.6 1.2 - - - +
771 ASN 5.2 2.5 - - - +
781 LYS 4.2 4.2 - - - +
791 PRO* 3.5 26.8 - - - +
286 GLU 2.9 11.8 + - - -
296 GLU* 3.4 8.1 + - - +
306 LYS 3.3 4.5 - - - +
316 GLU* 1.3 80.0 - - - +
336 LYS* 1.3 57.9 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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