Contacts of the helix formed by residues 389 - 401 (chain C) in PDB entry 3SRF
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 PHE 389 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C ALA* 3.9 14.6 - - - -
22C ALA* 4.0 6.3 - - + -
23C ASP* 3.5 26.9 - - - -
24C THR 3.9 0.4 - - - -
25C PHE* 3.7 38.1 - + + -
28C HIS* 3.7 36.0 + + + +
387C ALA 3.8 2.2 + - - -
388C MET* 1.3 68.9 - - - +
390C HIS* 1.3 54.5 + - - +
391C ARG* 3.2 33.9 - - - -
392C LYS* 3.0 38.4 + - + -
393C LEU* 2.8 37.6 + - + +
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Residues in contact with HIS 390 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA* 5.8 2.5 - - + +
43C ASN* 6.0 2.2 - - - -
385C GLU 3.2 26.3 + - - -
386C ALA* 4.4 7.0 + - - -
388C MET* 2.9 42.2 + - + +
389C PHE* 1.3 70.6 - - - +
391C ARG* 1.3 57.6 + - - +
393C LEU* 3.9 6.3 - - - +
394C PHE* 2.8 34.8 + - - +
420C TYR* 3.7 22.5 + - + +
444C ARG* 3.6 20.3 + - + +
445C PRO 4.2 4.5 - - - -
446C ARG* 3.2 59.2 + - + +
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Residues in contact with ARG 391 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C ALA* 3.4 21.6 + - - +
21C MET* 3.6 8.3 + - - +
23C ASP* 2.9 48.8 + - - +
389C PHE* 3.2 27.6 - - + -
390C HIS* 1.3 77.4 - - - +
392C LYS* 1.3 64.3 + - - +
394C PHE* 3.8 5.4 - - - +
395C GLU* 3.1 49.9 + - + +
420C TYR* 4.9 8.6 - - + -
446C ARG* 6.0 0.2 - - - +
398G VAL* 6.0 6.5 - - + -
399G ARG* 4.1 24.8 - - - +
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Residues in contact with LYS 392 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C PHE* 3.3 23.5 - - + +
389C PHE* 3.0 44.4 + - + +
391C ARG* 1.3 81.0 - - - +
393C LEU* 1.3 65.2 + - - +
395C GLU* 3.4 14.9 + - - +
396C GLU* 3.1 51.7 + - + +
25D PHE* 3.4 15.9 - - - +
392D LYS* 2.8 38.2 - - - +
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Residues in contact with LEU 393 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C ASN* 5.1 9.9 - - - +
353C ASP 6.1 0.4 - - - +
388C MET* 4.0 29.6 - - + -
389C PHE* 2.8 21.3 + - + +
390C HIS* 3.9 9.0 - - - +
392C LYS* 1.3 71.4 - - - +
394C PHE* 1.3 59.8 + - - +
396C GLU* 3.1 20.4 + - + +
397C LEU* 2.9 45.8 + - + +
444C ARG* 3.8 33.7 - - + +
26D LEU* 5.2 10.3 - - + -
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Residues in contact with PHE 394 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390C HIS 2.8 22.2 + - - +
391C ARG* 3.8 6.1 - - - +
393C LEU* 1.3 74.1 - - - +
395C GLU* 1.3 61.7 + - + +
397C LEU* 3.4 7.8 + - - +
398C VAL* 3.0 51.5 + - + +
413C MET* 3.3 30.1 - - + -
416C VAL* 3.7 24.2 - - + -
417C GLU* 3.4 29.4 - - + -
420C TYR* 3.7 18.2 - + + +
443C TYR* 3.4 38.8 - + + +
444C ARG* 5.9 0.8 - - - +
417G GLU* 4.5 7.4 - - - -
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Residues in contact with GLU 395 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391C ARG* 3.1 38.8 + - + +
392C LYS* 3.5 17.2 - - - +
393C LEU 3.3 0.2 - - - -
394C PHE* 1.3 83.6 - - + +
396C GLU* 1.3 58.2 + - + +
398C VAL* 3.6 7.5 + - - +
399C ARG* 3.0 28.9 + - - +
395G GLU* 3.1 49.5 - - + +
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Residues in contact with GLU 396 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392C LYS* 3.1 32.0 + - + +
393C LEU* 3.1 18.9 + - + +
395C GLU* 1.3 77.9 - - + +
397C LEU* 1.3 56.7 + - - +
399C ARG* 3.6 6.8 + - - +
400C ALA* 3.2 26.3 + - - +
24D THR* 3.5 26.0 - - + +
25D PHE* 2.7 41.6 + - - +
26D LEU* 3.2 27.8 + - + +
392D LYS* 5.4 0.3 - - - -
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Residues in contact with LEU 397 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317C ASN* 3.6 40.2 - - + +
318C ARG* 4.3 3.1 - - - +
393C LEU* 2.9 39.0 + - + +
394C PHE* 3.9 4.9 - - - +
396C GLU* 1.3 72.0 - - - +
398C VAL* 1.3 63.8 + - - +
399C ARG 3.3 0.2 - - - -
400C ALA* 3.5 3.6 + - - +
401C SER* 2.9 27.1 + - - -
442C ARG* 3.4 22.4 - - - +
443C TYR* 3.9 23.1 - - + -
444C ARG* 4.0 15.3 - - + +
26D LEU* 3.9 20.2 - - + -
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Residues in contact with VAL 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394C PHE* 3.0 51.3 + - + +
395C GLU* 3.7 7.0 - - - +
397C LEU* 1.3 75.7 - - - +
399C ARG* 1.3 63.9 + - - +
401C SER* 3.4 7.8 + - - -
402C SER* 3.2 24.1 + - - -
413C MET* 3.7 37.7 - - + -
443C TYR* 4.0 5.6 - - + -
391G ARG* 6.1 6.1 - - + -
395G GLU* 6.0 2.0 - - - +
417G GLU* 4.5 9.9 - - - +
421G LYS* 4.1 1.8 + - + +
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Residues in contact with ARG 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395C GLU 3.0 18.0 + - - +
396C GLU* 3.6 9.6 - - - +
398C VAL* 1.3 78.6 - - - +
400C ALA* 1.3 60.5 + - - +
402C SER* 2.7 31.8 + - - -
403C HIS* 4.9 1.4 - - - -
23D ASP* 4.2 16.2 + - - -
24D THR* 4.8 12.1 + - + +
21G MET* 3.2 26.7 + - - +
23G ASP* 3.3 38.9 + - - +
391G ARG* 3.9 25.4 - - - +
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Residues in contact with ALA 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318C ARG* 3.5 39.2 - - + +
396C GLU 3.2 13.9 + - - +
397C LEU* 4.0 4.7 - - - +
398C VAL 3.4 0.4 - - - -
399C ARG* 1.3 80.1 - - - +
401C SER* 1.3 57.5 + - - +
402C SER 3.4 0.4 - - - -
403C HIS* 3.2 23.1 + - - -
26D LEU* 4.6 6.1 - - + -
27D GLU* 5.6 3.1 - - - +
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Residues in contact with SER 401 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318C ARG 5.1 2.7 - - - -
397C LEU 2.9 15.2 + - - -
398C VAL 3.4 1.6 + - - -
399C ARG 3.3 0.2 - - - -
400C ALA* 1.3 77.3 - - - +
402C SER* 1.3 61.2 + - - +
403C HIS* 3.2 7.4 - - - -
404C SER* 3.1 20.0 + - - -
409C GLU* 3.6 13.7 - - - -
442C ARG* 4.4 16.2 - - - -
443C TYR* 2.8 22.0 + - - -
421G LYS* 2.8 24.2 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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