Contacts of the helix formed by residues 18 - 42 (chain 7) in PDB entry 6FF7
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 SER 18 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177 ALA* 1.3 82.3 - - - +
197 SER* 1.3 67.7 + - - +
207 SER* 3.2 9.0 + - - -
217 GLU 3.9 1.3 + - - +
227 SER* 3.4 19.2 + - - -
1064u GLU* 5.3 14.4 - - - -
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Residues in contact with SER 19 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302 A 5.2 11.7 - - - -
187 SER* 1.3 78.6 - - - +
207 SER* 1.3 56.4 + - - +
227 SER* 3.8 4.6 - - - -
237 ASN* 2.9 33.3 + - - +
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Residues in contact with SER 20 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187 SER* 3.2 6.6 - - - -
197 SER* 1.3 78.5 - - - +
217 GLU* 1.3 60.0 + - - +
237 ASN* 3.9 0.5 - - - +
247 ARG* 2.9 29.3 + - - +
1102u LYS 4.9 1.6 - - - +
1103u VAL* 4.3 30.2 - - - +
1105u GLU* 6.3 2.5 - - - -
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Residues in contact with GLU 21 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177 ALA* 3.7 25.1 - - + +
187 SER* 3.9 2.6 + - - -
207 SER* 1.3 79.1 - - - +
227 SER* 1.3 57.4 + - - +
247 ARG* 3.5 6.9 - - - +
257 ASP* 2.9 30.3 + - - +
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Residues in contact with SER 22 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177 ALA* 5.0 2.8 - - - +
187 SER 3.4 19.3 + - - -
197 SER* 3.8 6.1 - - - -
207 SER 3.2 0.6 - - - -
217 GLU* 1.3 79.8 - - - +
237 ASN* 1.3 57.6 + - - +
257 ASP* 3.4 5.0 + - - +
267 ARG* 2.9 25.7 + - - +
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Residues in contact with ASN 23 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197 SER* 2.9 17.6 + - - +
207 SER* 4.7 1.1 - - - +
227 SER* 1.3 74.1 - - - +
247 ARG* 1.3 59.4 + - - +
267 ARG* 3.6 11.4 - - + +
277 ARG* 2.9 28.4 + - - +
39L HIS* 6.2 4.3 - - + -
1103u VAL 5.7 3.8 - - - +
1104u GLN* 6.3 2.7 - - + -
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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 SER 2.9 20.5 + - - +
217 GLU* 3.5 9.9 - - - +
227 SER 3.3 0.2 - - - -
237 ASN* 1.3 76.8 - - - +
257 ASP* 1.3 58.0 + - - +
277 ARG* 3.3 6.2 + - - +
287 GLU* 3.0 27.8 + - - +
1102u LYS* 4.0 20.4 - - + +
1103u VAL 5.3 3.3 + - - +
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Residues in contact with ASP 25 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217 GLU 2.9 17.8 + - - +
227 SER* 3.8 4.9 - - - +
247 ARG* 1.3 75.5 - - - +
267 ARG* 1.3 57.2 + - - +
287 GLU* 3.5 6.8 + - - +
297 ARG* 2.9 30.8 + - - +
5498 MET* 6.3 2.9 - - + -
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Residues in contact with ARG 26 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227 SER 2.9 17.7 + - - +
237 ASN* 3.6 13.5 - - + +
257 ASP* 1.3 77.5 - - - +
277 ARG* 1.3 57.0 + - - +
297 ARG* 3.3 6.3 + - - +
307 LEU* 2.9 29.8 + - - +
36L SER 4.7 14.6 - - - +
37L LEU* 5.0 14.4 - - - +
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Residues in contact with ARG 27 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237 ASN 2.9 17.5 + - - +
247 ARG* 3.3 5.6 + - - +
267 ARG* 1.3 73.9 - - - +
287 GLU* 1.3 60.8 + - - +
307 LEU* 3.4 6.8 + - - +
317 ARG* 2.9 27.5 + - - +
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Residues in contact with GLU 28 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247 ARG 3.0 16.7 + - - +
257 ASP* 3.9 7.9 - - - +
277 ARG* 1.3 76.5 - - - +
297 ARG* 1.3 57.8 + - - +
317 ARG* 3.3 8.9 + - - +
327 GLN* 2.9 27.9 + - - +
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Residues in contact with ARG 29 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257 ASP 2.9 19.3 + - - +
267 ARG* 3.6 7.0 - - - +
287 GLU* 1.3 73.7 - - - +
307 LEU* 1.3 60.1 + - - +
327 GLN* 3.4 7.3 + - - +
337 LEU* 2.9 27.8 + - - +
37L LEU* 5.8 5.4 - - + -
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Residues in contact with LEU 30 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267 ARG 2.9 18.1 + - - +
277 ARG* 3.8 6.7 - - - +
297 ARG* 1.3 72.8 - - - +
317 ARG* 1.3 60.2 + - - +
337 LEU* 3.5 8.5 - - - +
347 ALA* 2.9 29.3 + - - +
667 GLU* 4.2 14.1 - - + +
37L LEU* 5.4 12.9 - - + +
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Residues in contact with ARG 31 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277 ARG 2.9 14.7 + - - +
287 GLU* 3.4 13.2 - - - +
307 LEU* 1.3 76.7 - - - +
327 GLN* 1.3 56.7 + - - +
347 ALA* 3.3 6.9 + - - +
357 LEU* 2.9 29.2 + - - +
667 GLU* 5.4 2.9 - - - -
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Residues in contact with GLN 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 15.6 + - - +
297 ARG* 3.7 7.9 - - - +
317 ARG* 1.3 75.3 - - - +
337 LEU* 1.3 56.6 + - - +
357 LEU* 3.8 6.3 - - - +
367 GLU* 2.9 31.5 + - - +
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Residues in contact with LEU 33 (chain 7).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297 ARG 2.9 18.3 + - - +
307 LEU* 3.5 9.6 - - - +
317 ARG 3.2 0.2 - - - -
327 GLN* 1.3 77.5 - - - +
347 ALA* 1.3 56.2 + - - +
367 GLU* 3.4 4.4 + - - +
377 THR* 3.0 30.4 + - - -
21L ALA* 5.7 6.5 - - + +
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Residues in contact with ALA 34 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307 LEU 2.9 18.1 + - - +
317 ARG* 3.7 5.8 - - - +
337 LEU* 1.3 76.1 - - - +
357 LEU* 1.3 57.4 + - - +
377 THR* 3.4 5.7 + - - -
387 ILE* 3.0 29.6 + - - +
667 GLU* 3.9 23.6 - - + +
707 LEU* 6.0 4.5 - - + -
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Residues in contact with LEU 35 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317 ARG 2.9 18.2 + - - +
327 GLN* 3.9 6.7 - - - +
347 ALA* 1.3 76.3 - - - +
367 GLU* 1.3 59.0 + - - +
387 ILE* 3.5 4.3 + - - +
397 ASP* 2.9 27.5 + - - +
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Residues in contact with GLU 36 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327 GLN 2.9 18.0 + - - +
337 LEU* 4.1 4.3 - - - +
357 LEU* 1.3 77.2 - - - +
377 THR* 1.3 58.4 + - - +
397 ASP* 3.5 8.5 - - + +
407 ILE* 2.9 28.4 + - - +
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Residues in contact with THR 37 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337 LEU 3.0 17.6 + - - -
347 ALA* 3.9 5.4 - - - -
367 GLU* 1.3 79.0 - - - +
387 ILE* 1.3 57.2 + - - +
407 ILE* 3.9 4.8 - - - +
417 ASN* 2.9 29.8 + - - +
21L ALA* 4.8 18.4 - - - -
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Residues in contact with ILE 38 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
347 ALA 3.0 17.6 + - - +
357 LEU* 4.2 4.0 - - - +
377 THR* 1.3 75.3 - - - +
397 ASP* 1.3 60.8 + - - +
417 ASN* 4.3 5.8 - - - +
427 LYS* 2.9 21.1 + - - -
437 ASP* 3.3 27.5 + - + +
467 PHE* 4.9 11.9 - - + -
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Residues in contact with ASP 39 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357 LEU 2.9 18.4 + - - +
367 GLU* 3.5 10.1 - - - +
377 THR 3.2 0.4 - - - -
387 ILE* 1.3 74.8 - - - +
407 ILE* 1.3 64.4 + - - +
427 LYS* 3.6 10.8 + - - +
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Residues in contact with ILE 40 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367 GLU 2.9 15.6 + - - +
377 THR* 4.0 5.6 - - - +
397 ASP* 1.3 79.3 - - - +
417 ASN* 1.3 61.2 + - - +
427 LYS* 3.3 4.0 + - - +
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Residues in contact with ASN 41 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377 THR 2.9 19.0 + - - +
387 ILE* 4.4 4.7 - - - -
407 ILE* 1.3 74.2 - - - +
427 LYS* 1.3 70.0 + - - +
437 ASP* 4.9 5.3 - - + +
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Residues in contact with LYS 42 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387 ILE 2.9 12.2 + - - -
397 ASP* 3.6 7.4 + - - +
407 ILE 3.2 7.0 - - - +
417 ASN* 1.3 81.1 - - - +
437 ASP* 1.3 59.3 + - - +
447 PRO* 3.7 3.5 - - - +
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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