Contacts of the helix formed by residues 26 - 48 (chain 7) in PDB entry 6CP3
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 ALA 26 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257 THR* 1.3 85.2 - - + +
277 THR* 1.3 56.3 + - - +
297 LEU* 3.2 26.5 + - + +
307 SER* 2.6 37.5 + - - +
4U LEU* 3.3 19.7 - - + +
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Residues in contact with THR 27 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187 SER* 5.5 6.5 - - - +
247 SER* 4.9 10.3 - - - -
257 THR 3.9 1.8 + - - +
267 ALA* 1.3 74.1 - - - +
287 GLN* 1.3 61.8 + - - +
307 SER* 3.0 20.6 + - - +
317 SER* 3.0 13.9 + - - -
4U LEU* 3.3 36.5 + - - +
6U PRO* 3.6 16.3 - - + +
123Z LEU* 5.6 10.5 - - + -
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Residues in contact with GLN 28 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157 VAL* 6.4 2.0 - - + -
247 SER* 3.5 30.6 + - - +
257 THR 4.4 8.7 + - - -
277 THR* 1.3 79.5 - - - +
297 LEU* 1.3 77.0 + - - +
317 SER* 2.6 25.1 + - - +
327 PHE* 2.8 18.5 + - - +
509B THR* 6.3 3.1 - - + -
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Residues in contact with LEU 29 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257 THR 5.0 5.4 - - - +
267 ALA* 3.2 28.4 + - + +
277 THR 3.1 0.6 - - - -
287 GLN* 1.3 92.3 - - - +
307 SER* 1.3 61.6 + - - +
327 PHE* 3.2 18.0 + - + +
337 LYS* 2.9 58.9 + - + +
1U VAL 5.2 2.2 - - - +
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Residues in contact with SER 30 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267 ALA* 2.6 21.6 + - - +
277 THR* 3.0 11.6 + - - -
297 LEU* 1.3 75.8 - - - +
317 SER* 1.3 59.1 + - - +
337 LYS* 3.1 11.7 + - - +
347 LYS* 3.0 25.9 + - - +
1U VAL 4.7 2.9 + - - -
2U SER 2.6 32.7 + - - -
3U THR* 4.8 6.3 - - - -
4U LEU* 4.1 4.5 + - - +
131Z VAL* 4.8 6.2 - - - +
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Residues in contact with SER 31 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117 ASP* 3.3 31.0 - - - -
157 VAL* 6.1 0.7 - - - +
277 THR 3.0 10.3 + - - -
287 GLN* 2.6 28.8 + - - +
307 SER* 1.3 74.8 - - - +
327 PHE* 1.3 58.0 + - - +
347 LYS* 3.2 16.4 + - - +
357 ARG* 2.9 28.3 + - - +
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Residues in contact with PHE 32 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287 GLN* 2.8 18.1 + - - +
297 LEU* 3.3 22.2 - - + +
307 SER 3.2 0.2 - - - -
317 SER* 1.3 78.9 + - - +
337 LYS* 1.3 64.8 + - + +
357 ARG* 3.3 39.4 + - + +
367 ASN* 2.8 39.2 + - + +
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Residues in contact with LYS 33 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297 LEU* 2.9 41.4 + - + +
307 SER* 3.1 8.5 + - - +
327 PHE* 1.3 82.4 - - + +
347 LYS* 1.3 62.3 + - - +
367 ASN* 3.2 10.7 + - + +
377 ASP* 2.9 28.9 + - - +
1U VAL* 3.0 53.3 - - + +
131Z VAL* 5.5 4.5 - - + -
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Residues in contact with LYS 34 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77 ALA* 5.0 5.0 + - - +
87 ASN* 3.1 33.1 - - - +
117 ASP* 3.3 32.4 + - - +
307 SER 3.0 8.7 + - - +
317 SER* 3.2 24.3 + - - +
337 LYS* 1.3 73.4 - - - +
357 ARG* 1.3 60.6 + - - +
377 ASP* 2.9 19.9 - - - +
387 GLU* 2.9 30.1 + - - +
127Z SER* 4.3 19.3 - - - +
130Z THR* 3.7 24.7 + - - +
131Z VAL* 3.6 27.0 - - + +
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Residues in contact with ARG 35 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317 SER 2.9 18.5 + - - +
327 PHE* 3.3 42.8 - - - +
347 LYS* 1.3 76.1 - - - +
367 ASN* 1.3 67.7 + - - +
387 GLU* 4.7 2.9 - - - -
397 ALA* 2.9 54.3 + - + +
469B SER* 4.6 23.3 + - - +
472B SER* 4.4 15.6 + - - +
473B TYR* 5.2 17.5 - - + +
476B SER* 5.0 4.8 + - - +
477B ASN* 6.0 2.5 - - - +
506B PHE* 5.9 7.4 - - + -
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Residues in contact with ASN 36 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327 PHE* 2.8 26.3 + - + +
337 LYS* 3.2 15.9 + - - +
357 ARG* 1.3 88.8 + - - +
377 ASP* 1.3 59.9 + - + +
397 ALA* 3.8 1.6 - - - +
407 ARG* 2.9 28.4 + - - +
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Residues in contact with ASP 37 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337 LYS 2.9 10.9 + - - +
347 LYS* 2.9 23.2 - - - +
367 ASN* 1.3 81.7 - - + +
387 GLU* 1.3 57.1 + - - +
407 ARG* 3.6 28.6 + - - +
417 ARG* 2.9 26.9 + - - +
130Z THR 4.8 0.7 - - - +
131Z VAL* 3.3 27.3 - - - +
134Z GLU* 3.1 23.5 - - + +
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Residues in contact with GLU 38 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47 LYS* 3.5 20.8 - - - +
87 ASN* 4.3 9.6 + - - +
347 LYS* 2.9 29.5 + - - +
357 ARG* 4.3 2.9 - - - +
377 ASP* 1.3 75.0 + - - +
397 ALA* 1.3 63.8 + - - +
417 ARG* 3.1 47.4 + - - +
427 GLN* 3.5 2.8 + - - +
476B SER* 3.5 21.5 + - - +
477B ASN* 3.9 14.0 - - - +
130Z THR* 4.8 14.4 - - - +
134Z GLU* 3.3 22.6 - - - +
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Residues in contact with ALA 39 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357 ARG* 2.9 32.0 + - - +
367 ASN 4.0 2.2 - - - +
387 GLU* 1.3 76.1 - - - +
407 ARG* 1.3 61.3 + - - +
427 GLN* 3.4 16.7 + - - +
437 LEU* 3.3 19.2 - - + +
472B SER* 3.8 30.2 + - - +
476B SER* 3.4 13.7 + - - +
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Residues in contact with ARG 40 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367 ASN* 2.9 22.9 + - - +
377 ASP* 3.6 26.7 + - - +
387 GLU 3.2 0.2 - - - -
397 ALA* 1.3 77.3 - - - +
417 ARG* 1.3 59.3 + - - +
437 LEU* 3.4 19.0 - - + +
447 LEU* 3.0 57.0 + - - +
134Z GLU* 4.6 9.2 + - - -
137Z ALA* 4.2 7.5 - - - +
138Z PHE* 4.0 34.7 - - - +
141Z LYS* 5.0 2.5 - - - +
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Residues in contact with ARG 41 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47 LYS* 3.5 30.7 - - - +
377 ASP 2.9 15.8 + - - +
387 GLU* 3.1 47.1 + - - +
407 ARG* 1.3 80.0 - - - +
427 GLN* 1.3 84.1 + - - +
447 LEU* 3.5 8.4 - - - +
457 GLU* 2.9 34.1 + - - +
475B LYS 5.6 0.4 + - - -
476B SER* 4.6 8.9 + - - +
134Z GLU* 3.4 25.3 + - + +
137Z ALA* 3.6 27.1 - - + +
140Z LEU* 5.8 0.2 - - - +
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Residues in contact with GLN 42 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387 GLU 3.7 8.1 - - - +
397 ALA* 3.4 22.4 + - - +
417 ARG* 1.3 98.5 - - - +
437 LEU* 1.3 84.8 + - - +
457 GLU* 3.3 21.0 - - - +
467 LEU* 2.9 30.7 + - - +
472B SER* 5.1 4.9 + - - -
475B LYS* 3.7 47.3 + - - +
476B SER* 4.2 6.7 - - - +
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Residues in contact with LEU 43 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397 ALA* 3.3 17.5 - - + +
407 ARG* 3.4 21.1 - - + +
427 GLN* 1.3 91.6 - - - +
447 LEU* 1.3 58.9 + - + +
467 LEU* 4.4 5.6 - - - +
477 GLN* 2.7 46.7 + - + +
472B SER* 5.9 2.7 - - - +
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Residues in contact with LEU 44 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407 ARG* 3.0 54.5 + - - +
417 ARG* 3.5 7.0 - - - +
427 GLN 3.2 0.2 - - - -
437 LEU* 1.3 85.6 - - + +
457 GLU* 1.3 60.6 + - - +
477 GLN* 3.6 10.7 + - - +
487 SER* 3.7 15.1 + - - -
137Z ALA* 3.5 19.5 - - + +
140Z LEU* 4.1 14.1 - - + -
141Z LYS* 3.6 39.7 - - + +
144Z VAL* 4.2 10.1 - - + +
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Residues in contact with GLU 45 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417 ARG* 2.9 22.2 + - - +
427 GLN* 3.3 24.9 - - - +
447 LEU* 1.3 77.2 - - - +
467 LEU* 1.3 70.7 + - - +
487 SER* 4.1 11.3 + - - +
140Z LEU* 4.3 21.5 - - + -
144Z VAL* 6.0 0.2 - - - -
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Residues in contact with LEU 46 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427 GLN* 2.9 21.0 + - - +
437 LEU* 4.4 4.5 - - - +
457 GLU* 1.3 86.6 - - - +
477 GLN* 1.3 64.6 + - - +
487 SER 3.4 5.4 - - - +
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Residues in contact with GLN 47 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437 LEU* 2.7 27.8 + - + +
447 LEU* 3.6 6.5 + - - +
457 GLU 3.3 0.4 - - - -
467 LEU* 1.3 80.4 - - - +
487 SER* 1.3 66.0 + - - +
497 GLN* 3.6 14.4 + - - +
144Z VAL* 4.1 19.8 - - - +
148Z HIS* 4.8 14.8 - - - -
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Residues in contact with SER 48 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447 LEU 3.7 7.5 + - - -
457 GLU* 4.1 7.8 + - - +
467 LEU 3.4 7.4 - - - +
477 GLN* 1.3 90.0 - - - +
497 GLN* 1.3 84.7 + - - +
507 PRO* 4.8 0.7 - - - +
517 THR* 3.3 16.8 - - - +
144Z VAL* 3.7 33.2 + - - +
147Z ALA* 5.8 0.2 - - - +
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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