Contacts of the helix formed by residues 389 - 401 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19H ALA 4.6 0.4 - - - -
20H ALA* 3.9 22.0 - - - +
22H ALA* 4.3 1.3 - - + -
23H ASP* 3.4 32.1 - - - -
24H THR 3.6 28.5 - - - -
25H PHE* 3.7 15.7 - + + -
28H HIS* 3.5 37.2 + + + +
388H MET* 1.3 68.8 - - - +
390H HIS* 1.3 61.7 + - - +
391H ARG* 4.0 14.4 - - + -
392H LYS* 3.7 41.5 - - + -
393H LEU* 3.0 29.9 + - - +
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Residues in contact with HIS 390 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20H ALA* 5.6 4.0 - - + +
43H ASN* 6.0 1.8 - - - -
385H GLU 3.4 23.6 + - - -
386H ALA* 4.6 7.7 + - - -
388H MET* 2.9 37.3 + - + +
389H PHE* 1.3 72.8 - - - +
391H ARG* 1.3 56.0 + - - +
393H LEU* 2.9 11.1 + - - +
394H PHE* 2.7 34.8 + - - +
420H TYR* 4.2 16.7 + - + +
444H ARG* 4.0 16.5 + - + +
445H PRO 4.5 3.1 - - - -
446H ARG* 3.4 68.7 + - + +
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Residues in contact with ARG 391 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
398D VAL* 6.1 6.3 - - + -
399D ARG* 4.5 23.3 - - - +
20H ALA* 3.0 28.0 + - - +
21H MET* 3.4 16.2 + - - +
23H ASP* 3.2 47.2 + - - +
389H PHE* 3.5 12.1 - - + -
390H HIS* 1.3 77.7 - - - +
392H LYS* 1.3 62.0 + - - +
394H PHE* 3.6 6.3 + - + +
395H GLU* 3.2 49.5 + - + +
417H GLU* 5.8 4.3 - - - +
420H TYR* 5.4 7.2 - - + -
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Residues in contact with LYS 392 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25G PHE* 4.1 6.4 - - + +
392G LYS* 3.0 46.0 - - - +
396G GLU* 4.7 1.3 + - - -
25H PHE* 3.5 21.6 - - + +
389H PHE* 3.6 43.6 + - + +
390H HIS 3.2 0.4 - - - -
391H ARG* 1.3 78.4 - - - +
393H LEU* 1.3 62.7 + - - +
395H GLU* 3.7 13.2 + - - +
396H GLU* 3.1 56.9 + - + +
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Residues in contact with LEU 393 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LEU* 4.9 12.3 - - + -
317H ASN* 5.6 5.4 - - + +
353H ASP 5.6 5.6 - - - +
354H GLY* 6.3 0.7 - - - -
388H MET* 3.9 31.6 - - + -
389H PHE 3.0 18.5 + - - +
390H HIS* 2.9 12.4 + - - +
392H LYS* 1.3 74.5 - - - +
394H PHE* 1.3 64.4 + - - +
396H GLU* 3.3 12.5 + - + +
397H LEU* 2.9 49.5 + - + +
444H ARG* 3.8 30.1 - - + +
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Residues in contact with PHE 394 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417D GLU* 3.7 12.3 - - - -
390H HIS 2.7 18.9 + - - +
391H ARG* 3.9 5.4 - - + +
393H LEU* 1.3 72.3 - - - +
395H GLU* 1.3 64.3 + - + +
397H LEU* 3.2 8.8 + - - +
398H VAL* 2.8 57.3 + - + +
413H MET* 3.5 32.3 - - + -
416H VAL* 3.9 14.6 - - + -
417H GLU* 3.5 32.1 - - + -
420H TYR* 3.8 23.3 + + + +
443H TYR* 3.4 31.6 - - + -
444H ARG* 5.9 0.8 - - - +
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Residues in contact with GLU 395 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395D GLU* 3.1 39.2 - - + +
391H ARG* 3.2 38.5 + - + +
392H LYS* 3.8 12.5 - - - +
394H PHE* 1.3 86.6 - - + +
396H GLU* 1.3 60.1 + - + +
398H VAL* 3.2 6.6 + - - +
399H ARG* 2.9 29.5 + - - +
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Residues in contact with GLU 396 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G THR* 3.6 33.9 - - + +
25G PHE* 2.9 34.6 + - - +
26G LEU* 3.4 24.0 + - + +
392H LYS* 3.1 43.5 + - + +
393H LEU* 3.8 11.1 + - + +
395H GLU* 1.3 80.7 - - + +
397H LEU* 1.3 57.9 + - - +
399H ARG* 4.0 6.2 - - - +
400H ALA* 3.2 25.6 + - - +
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Residues in contact with LEU 397 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26G LEU* 4.0 17.5 - - + -
317H ASN* 3.4 41.1 - - + +
318H ARG* 4.2 3.4 - - - +
393H LEU* 2.9 45.6 + - + +
394H PHE* 3.7 3.6 - - - +
396H GLU* 1.3 75.4 - - - +
398H VAL* 1.3 62.1 + - - +
400H ALA* 3.6 3.8 + - - +
401H SER* 2.9 25.5 + - - -
442H ARG* 3.4 23.4 + - - +
443H TYR* 4.0 16.0 - - + -
444H ARG* 3.9 14.8 - - + -
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Residues in contact with VAL 398 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
391D ARG* 6.3 2.9 - - + -
417D GLU* 4.5 7.6 - - - +
421D LYS* 4.7 1.3 + - + -
394H PHE* 2.8 53.6 + - + +
395H GLU* 3.6 7.0 - - - +
397H LEU* 1.3 75.4 - - - +
399H ARG* 1.3 60.4 + - - +
401H SER* 3.2 9.2 + - - -
402H SER* 3.0 26.3 + - - -
413H MET* 3.7 34.5 - - + -
443H TYR* 4.1 4.3 - - + -
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Residues in contact with ARG 399 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D MET 4.9 3.4 + - - -
22D ALA 4.5 1.6 + - - -
23D ASP* 2.6 46.8 + - - +
391D ARG* 3.6 28.9 - - - +
23G ASP* 3.8 21.6 + - - -
24G THR* 3.9 19.1 + - - -
395H GLU 2.9 16.0 + - - +
396H GLU* 4.0 6.5 - - - +
397H LEU 3.4 0.2 - - - -
398H VAL* 1.3 77.3 - - - +
400H ALA* 1.3 60.0 + - - +
402H SER* 2.9 28.4 + - - +
403H HIS* 5.0 2.9 + - - -
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Residues in contact with ALA 400 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26G LEU* 4.0 9.2 - - + -
318H ARG* 3.6 38.2 - - + +
396H GLU 3.2 18.0 + - - +
397H LEU* 3.8 6.7 - - - +
398H VAL 3.3 0.4 - - - -
399H ARG* 1.3 78.8 - - - +
401H SER* 1.3 58.2 + - - +
402H SER 3.5 0.4 - - - -
403H HIS* 3.9 19.2 + - - -
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Residues in contact with SER 401 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421D LYS* 2.5 33.5 + - - -
318H ARG 5.3 0.2 - - - -
397H LEU 2.9 17.1 + - - -
398H VAL* 3.2 5.1 + - - -
399H ARG 3.2 0.4 - - - -
400H ALA* 1.3 77.4 - - - +
402H SER* 1.3 62.1 + - - +
403H HIS* 3.4 4.5 - - - -
404H SER* 3.2 13.3 + - - -
409H GLU* 3.7 6.1 - - - -
442H ARG* 4.1 17.0 - - - -
443H TYR* 3.1 24.7 + - - -
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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
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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) + - + + + + + -
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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