Contacts of the helix formed by residues 13 - 32 (chain 7) 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 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116 PRO* 3.8 38.3 - - + +
126 ALA 3.5 15.5 - - - +
136 THR* 4.6 2.9 - - + -
117 PRO 3.9 9.2 - - - +
127 ALA* 1.3 79.3 - - - +
147 ALA* 1.3 65.3 + - - +
157 GLU* 3.3 17.9 + - - +
167 THR* 3.0 18.7 + - - +
177 GLN* 3.0 21.4 + - - +
437 PHE* 4.8 7.3 - - + -
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Residues in contact with ALA 14 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116 PRO* 5.7 0.8 - - - +
126 ALA 4.3 4.2 + - - -
396 LYS* 4.7 20.6 - - - +
137 THR* 1.3 74.8 - - - +
157 GLU* 1.3 57.3 + - - +
177 GLN* 3.2 9.2 + - - +
187 HIS* 2.9 28.1 + - - +
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Residues in contact with GLU 15 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137 THR* 3.1 11.0 + - - +
147 ALA* 1.3 75.8 - - - +
167 THR* 1.3 64.1 + - - +
187 HIS* 3.2 10.3 + - + +
197 ILE* 3.0 41.3 + - + +
537 TYR* 4.1 17.8 + - - -
717 GLN* 5.6 1.7 - - - +
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Residues in contact with THR 16 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127 ALA* 3.8 9.2 - - + -
137 THR* 3.0 30.3 + - - -
157 GLU* 1.3 77.1 - - - +
177 GLN* 1.3 62.4 + - - +
197 ILE* 3.2 11.1 + - + +
207 ALA* 3.0 23.7 + - - +
407 ALA* 3.8 7.4 - - + -
437 PHE* 3.5 36.4 - - + -
537 TYR* 6.3 0.2 - - + -
557 ILE* 3.7 31.0 - - + +
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Residues in contact with GLN 17 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127 ALA* 6.2 0.2 - - + -
137 THR 3.0 12.0 + - - +
147 ALA* 3.6 11.9 - - - +
157 GLU 3.2 0.2 - - - -
167 THR* 1.3 76.5 - - - +
187 HIS* 1.3 57.6 + - - +
207 ALA* 3.4 5.7 + - - +
217 ASP* 2.8 68.3 + - - +
387 PHE 2.8 21.9 + - - -
397 LYS* 3.6 8.9 - - - +
407 ALA* 2.8 34.1 + - + +
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Residues in contact with HIS 18 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147 ALA 2.9 14.0 + - - +
157 GLU* 3.2 15.5 + - + +
177 GLN* 1.3 77.2 - - - +
197 ILE* 1.3 71.1 + - + +
217 ASP* 3.3 9.9 + - - +
227 GLN* 3.1 59.6 + - + +
807 LEU* 4.8 6.4 - - + +
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Residues in contact with ILE 19 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157 GLU* 3.0 34.7 + - + +
167 THR* 3.6 9.6 - - - +
187 HIS* 1.3 81.8 - - + +
207 ALA* 1.3 63.4 + - - +
227 GLN* 3.2 13.9 + - - +
237 VAL* 3.4 13.2 + - - +
537 TYR* 3.8 43.7 - - + -
557 ILE* 3.7 17.9 - - + -
697 VAL* 3.9 25.6 - - + -
717 GLN* 4.6 7.4 - - - +
807 LEU* 4.1 21.4 - - + +
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Residues in contact with ALA 20 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167 THR 3.0 15.3 + - - +
177 GLN* 3.7 7.4 - - - +
197 ILE* 1.3 79.4 - - - +
217 ASP* 1.3 61.6 + - - +
237 VAL* 3.1 21.0 + - - +
247 ARG 3.1 10.2 + - - -
387 PHE* 3.3 25.5 - - + -
407 ALA* 4.5 9.0 - - + -
557 ILE* 4.2 6.0 - - + +
577 VAL* 4.3 17.3 - - + -
677 LEU* 4.3 5.6 - - + -
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Residues in contact with ASP 21 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177 GLN* 2.8 58.3 + - - +
187 HIS* 3.6 9.3 - - - +
207 ALA* 1.3 72.2 - - - +
227 GLN* 1.3 66.8 + - + +
237 VAL 3.2 0.9 + - - -
247 ARG* 3.3 24.0 + - - +
257 SER 4.8 1.2 + - - -
387 PHE* 4.2 8.3 - - - +
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Residues in contact with GLN 22 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187 HIS* 3.1 49.0 + - + +
197 ILE 3.6 8.1 - - - +
207 ALA 3.1 0.6 - - - -
217 ASP* 1.3 79.8 + - - +
237 VAL* 1.3 62.0 + - - +
257 SER* 5.1 4.6 + - - -
267 GLN* 3.9 9.5 + - - -
807 LEU* 3.7 25.8 + - + +
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Residues in contact with VAL 23 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197 ILE 3.8 9.0 - - - +
207 ALA 3.1 14.4 + - - +
227 GLN* 1.3 80.2 - - - +
247 ARG* 1.3 66.0 + - - +
257 SER 3.3 2.9 - - - -
267 GLN* 3.0 30.4 + - - +
277 LEU* 3.2 12.0 + - + +
387 PHE* 5.4 0.4 - - + -
677 LEU* 3.9 25.4 - - + -
697 VAL* 3.9 33.7 - - + -
807 LEU* 4.0 11.7 - - + +
827 LEU* 4.0 23.2 - - + +
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Residues in contact with ARG 24 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207 ALA 3.1 5.4 + - - -
217 ASP* 3.3 21.0 + - - +
237 VAL* 1.3 76.5 - - - +
257 SER* 1.3 58.2 + - - +
277 LEU* 3.2 3.8 + - - +
287 GLU* 2.9 54.0 + - + +
357 PHE* 2.3 39.8 + - - +
367 PRO 2.7 16.4 + - - -
387 PHE* 3.5 57.5 - - + +
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Residues in contact with SER 25 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217 ASP 4.8 1.0 + - - -
227 GLN 5.1 5.2 + - - -
237 VAL 3.3 0.2 - - - -
247 ARG* 1.3 78.1 - - - +
267 GLN* 1.3 63.7 + - - +
287 GLU* 3.7 14.6 + - - +
297 GLU* 2.9 30.1 + - - +
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Residues in contact with GLN 26 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227 GLN 3.9 15.8 + - - -
237 VAL* 3.0 12.4 + - - +
257 SER* 1.3 78.8 + - - +
277 LEU* 1.3 64.6 + - - +
297 GLU* 3.4 8.5 + - - +
307 LYS* 3.0 25.3 + - - +
797 PRO* 6.1 0.2 - - - +
807 LEU 3.4 21.6 + - - -
817 THR* 3.8 4.5 - - - +
827 LEU* 2.9 42.8 + - + +
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Residues in contact with LEU 27 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237 VAL* 3.2 8.4 + - + +
247 ARG* 3.5 8.1 - - - +
267 GLN* 1.3 78.4 - - - +
287 GLU* 1.3 58.2 + - - +
307 LYS* 3.2 2.0 + - - -
317 GLU* 2.8 39.1 + - + +
357 PHE* 3.5 29.4 - - + -
387 PHE* 3.6 26.9 - - + -
657 VAL* 4.1 18.6 - - + -
677 LEU* 4.1 5.4 - - + -
827 LEU* 3.8 11.2 - - + +
857 TYR* 3.7 48.7 - - + -
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Residues in contact with GLU 28 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247 ARG* 2.9 47.3 + - - +
257 SER* 3.7 16.6 + - - +
277 LEU* 1.3 77.6 - - - +
297 GLU* 1.3 56.1 + - - +
327 ASN* 2.9 25.5 + - - -
337 LYS 3.2 29.6 + - - +
347 LYS* 3.7 25.7 + - + +
357 PHE* 3.2 27.2 + - + -
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Residues in contact with GLU 29 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257 SER 2.9 18.1 + - - +
267 GLN* 3.7 7.7 - - - +
277 LEU 3.3 0.2 - - - -
287 GLU* 1.3 75.2 - - - +
307 LYS* 1.3 87.1 + - - +
327 ASN* 3.3 13.4 + - - +
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Residues in contact with LYS 30 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267 GLN 3.0 18.5 + - - +
277 LEU 3.2 2.7 + - - +
297 GLU* 1.3 95.5 + - - +
317 GLU* 1.3 63.4 + - - +
327 ASN* 3.5 1.2 + - - +
827 LEU* 5.8 0.7 - - + -
857 TYR* 3.2 32.3 - - + +
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Residues in contact with GLU 31 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277 LEU* 2.8 32.6 + - + +
287 GLU 4.3 0.7 - - - +
307 LYS* 1.3 75.6 - - - +
327 ASN* 1.3 69.2 + - - +
337 LYS* 3.4 28.9 + - + +
357 PHE* 4.3 11.7 - - + -
857 TYR* 2.6 34.9 + - + +
877 THR* 4.0 14.7 - - + +
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Residues in contact with ASN 32 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287 GLU 2.9 11.2 + - - -
297 GLU* 3.3 8.2 + - - +
307 LYS 3.3 4.3 - - - +
317 GLU* 1.3 80.2 - - - +
337 LYS* 1.3 58.7 + - - +
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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) + - + + + + + -
------------------------------------------------------------
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