Contacts of the helix formed by residues 385 - 404 (chain A) in PDB entry 3RFU
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 385 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197A LEU* 5.2 0.4 - - - -
383A PRO* 3.2 1.0 - - - +
384A CYS* 1.3 80.4 - - - +
386A LEU* 1.3 52.8 + - - +
387A GLY 3.0 5.6 - - - -
388A LEU* 2.7 37.7 + - + +
389A ALA* 3.3 8.5 + - - +
685A ALA* 3.9 14.6 - - + +
720A SER* 3.6 42.2 - - - +
721A SER* 4.2 5.6 - - - +
724A VAL* 4.3 6.9 - - + +
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Residues in contact with LEU 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MET* 3.3 37.7 - - + +
151A LEU* 3.8 13.2 - - + -
152A ILE* 3.7 18.6 - - + -
336A ALA* 5.0 7.4 - - + +
340A SER* 3.8 22.0 - - - +
383A PRO* 3.5 34.6 + - + +
385A ALA* 1.3 76.2 - - - +
387A GLY* 1.3 64.9 + - - +
388A LEU 3.2 0.7 + - - -
389A ALA* 3.8 15.8 + - - +
390A THR* 4.6 3.5 + - - -
391A PRO* 5.0 1.0 - - - +
682A LEU* 4.4 15.2 - - + +
685A ALA* 3.8 16.5 - - + +
686A PHE* 3.9 8.5 - - + -
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Residues in contact with GLY 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A MET* 4.6 7.2 - - - -
198A VAL* 4.6 12.8 - - - -
201A GLY* 2.9 30.9 - - - -
202A GLN* 5.6 2.2 + - - -
384A CYS 3.6 6.8 + - - -
385A ALA 2.8 2.4 + - - -
386A LEU* 1.3 90.2 - - - +
388A LEU* 1.3 59.4 + - - +
391A PRO* 3.1 12.7 - - - +
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A LEU* 3.5 43.3 - - + +
200A LEU* 3.8 26.9 - - + -
201A GLY* 3.7 15.7 - - - +
204A LEU* 4.5 9.4 - - + -
384A CYS 4.8 2.2 - - - +
385A ALA* 2.7 15.8 + - + +
387A GLY* 1.3 80.6 - - - +
389A ALA* 1.3 67.0 + - - +
391A PRO* 3.1 4.7 - - - +
392A MET* 2.9 43.7 + - + +
721A SER* 5.8 6.3 - - - +
724A VAL* 4.5 7.2 - - + -
725A ILE* 5.2 13.2 - - + -
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Residues in contact with ALA 389 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A ALA 3.3 9.2 + - - +
386A LEU* 3.8 11.6 + - - +
387A GLY 3.7 1.0 - - - -
388A LEU* 1.3 79.0 - - - +
390A THR* 1.3 67.9 + - - +
392A MET* 3.0 7.6 + - - +
393A SER* 3.1 13.5 + - - -
678A ILE* 4.8 1.1 - - - +
681A ASN* 3.5 34.7 + - + +
682A LEU* 4.0 22.2 - - + +
685A ALA* 5.2 0.4 - - + -
724A VAL* 4.1 11.3 - - + +
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Residues in contact with THR 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A ARG* 4.1 16.2 - - - +
334A ARG* 5.6 10.6 - - + +
335A LEU* 5.8 0.9 + - - +
336A ALA* 4.5 18.3 + - - +
386A LEU 4.6 2.8 + - - -
389A ALA* 1.3 79.4 - - - +
391A PRO* 1.3 73.9 - - + +
393A SER* 3.1 2.4 + - - -
394A ILE* 3.0 34.2 + - + +
415A GLU* 4.4 5.4 - - - +
678A ILE* 3.9 35.9 - - + +
682A LEU* 4.7 4.9 - - - +
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Residues in contact with PRO 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
201A GLY* 4.2 7.6 - - - +
204A LEU* 3.9 24.4 - - + +
205A GLU* 4.0 19.5 - - + +
208A ALA* 5.3 3.3 - - + +
209A ARG* 4.9 5.8 - - - +
386A LEU 5.0 1.1 - - - +
387A GLY 3.1 22.7 - - - +
388A LEU* 3.1 21.5 - - - +
389A ALA 3.4 0.2 - - - -
390A THR* 1.3 96.9 - - + +
392A MET* 1.3 55.5 - - + +
394A ILE* 3.3 9.2 + - + +
395A MET* 3.0 31.2 + - - +
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Residues in contact with MET 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 4.5 16.6 - - + -
388A LEU* 2.9 41.7 + - + +
389A ALA* 3.6 3.1 - - - +
391A PRO* 1.3 74.7 - - - +
393A SER* 1.3 66.6 + - - +
395A MET* 3.4 21.7 - - + +
396A VAL* 3.0 28.3 + - - +
724A VAL* 4.6 4.3 - - + -
725A ILE* 4.0 45.5 - - + +
728A ALA* 4.0 17.4 - - + +
729A LEU* 5.4 6.1 - - + -
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Residues in contact with SER 393 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
389A ALA 3.1 4.4 + - - -
390A THR 3.6 2.2 - - - -
392A MET* 1.3 77.3 - - - +
394A ILE* 1.3 60.0 + - - +
396A VAL* 3.1 10.4 - - - +
397A GLY* 3.0 26.3 + - - -
674A THR* 4.2 14.7 - - - -
677A ASN* 2.9 13.6 + - - -
678A ILE* 3.3 33.2 + - - +
681A ASN* 2.6 31.2 + - - +
728A ALA* 4.4 1.5 - - - +
731A LEU* 5.5 0.2 - - - -
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Residues in contact with ILE 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA* 4.5 16.8 - - + +
209A ARG* 4.2 9.9 - - - +
390A THR* 3.0 24.6 + - + +
391A PRO* 3.5 9.0 - - + +
392A MET 3.1 0.2 - - - -
393A SER* 1.3 76.1 - - - +
395A MET* 1.3 66.6 + - - +
397A GLY* 3.3 1.3 + - - -
398A VAL* 3.0 41.0 + - + +
411A ALA* 3.7 26.5 - - + +
414A LEU* 4.5 10.2 - - + +
415A GLU* 4.3 17.9 - - + +
674A THR* 4.9 7.9 - - - +
678A ILE* 3.8 23.3 - - + -
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Residues in contact with MET 395 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A LEU* 4.4 30.5 - - - +
207A LYS* 6.0 6.5 - - - +
208A ALA* 5.3 10.1 - - + +
391A PRO 3.0 19.4 + - - +
392A MET* 3.4 26.0 - - + +
394A ILE* 1.3 74.7 - - - +
396A VAL* 1.3 62.3 + - + +
398A VAL* 3.0 25.3 - - + +
399A GLY* 3.0 7.3 + - - -
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Residues in contact with VAL 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A MET 3.0 20.9 + - - +
393A SER* 3.1 14.8 - - - +
395A MET* 1.3 80.1 - - + +
397A GLY* 1.3 65.1 + - - +
399A GLY* 3.2 4.0 + - - -
400A LYS* 3.1 19.9 + - - +
728A ALA* 3.7 24.2 - - + +
729A LEU* 4.9 2.7 - - + -
731A LEU* 3.5 28.3 - - + +
732A LYS* 3.8 24.5 - - + -
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Residues in contact with GLY 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393A SER 3.0 12.1 + - - -
394A ILE 3.7 0.7 - - - -
395A MET 3.2 0.2 - - - -
396A VAL* 1.3 80.8 - - - +
398A VAL* 1.3 58.7 + - - +
399A GLY 3.0 1.6 - - - -
400A LYS* 2.8 21.0 + - - +
401A GLY* 3.0 12.1 + - - -
414A LEU* 4.4 7.6 - - - -
670A LEU* 4.1 4.7 - - - +
674A THR* 4.1 11.9 - - - -
731A LEU* 3.9 16.8 - - - -
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Residues in contact with VAL 398 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A ALA* 6.5 0.4 - - + -
394A ILE* 3.0 25.2 + - + +
395A MET* 3.0 26.9 - - + +
397A GLY* 1.3 75.7 - - - +
399A GLY* 1.3 56.8 + - - +
402A ALA* 2.8 33.5 + - - +
406A VAL 4.7 0.3 - - - +
408A ILE* 3.7 45.7 + - + +
411A ALA* 5.7 0.2 - - - -
414A LEU* 4.0 10.1 - - + +
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Residues in contact with GLY 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A MET 3.0 14.4 + - - -
396A VAL* 3.5 6.1 - - - -
397A GLY 3.0 1.2 - - - -
398A VAL* 1.3 80.2 - - - +
400A LYS* 1.3 55.2 + - - +
402A ALA* 4.0 4.2 - - - +
403A GLN* 3.0 27.9 + - - +
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Residues in contact with LYS 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396A VAL 3.1 11.2 + - - +
397A GLY* 2.8 11.9 + - - +
399A GLY* 1.3 75.1 - - - +
401A GLY* 1.3 66.7 + - - +
403A GLN* 2.8 44.8 + - - +
404A SER* 3.1 7.6 + - - -
670A LEU* 4.3 9.0 - - + -
731A LEU* 5.2 4.7 - - + +
732A LYS* 3.3 48.9 + - + +
733A ARG 4.2 1.1 - - - +
734A VAL* 3.9 33.5 - - - +
736A LEU* 4.1 21.5 - - + +
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Residues in contact with GLY 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A GLY 3.0 11.7 + - - -
398A VAL 4.3 0.4 - - - -
400A LYS* 1.3 75.4 - - - +
402A ALA* 1.3 54.9 + - - +
404A SER* 2.6 29.0 + - - -
406A VAL* 2.9 38.3 + - - -
408A ILE* 4.7 3.4 - - - -
670A LEU* 4.5 10.6 - - - +
736A LEU* 4.5 5.6 - - - -
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Residues in contact with ALA 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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398A VAL 2.8 22.6 + - - +
399A GLY* 4.1 5.2 - - - +
401A GLY* 1.3 73.5 - - - +
403A GLN* 1.3 61.2 - - - +
404A SER 3.2 0.3 + - - -
405A GLY* 3.4 8.7 + - - -
406A VAL 2.9 12.3 + - - +
407A LEU* 3.6 22.6 - - + +
408A ILE 5.5 0.7 - - - +
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Residues in contact with GLN 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A GLY 3.0 18.6 + - - +
400A LYS* 2.8 44.6 + - - +
402A ALA* 1.3 77.6 - - - +
404A SER* 1.3 56.5 + - - +
405A GLY 3.6 0.9 + - - -
734A VAL* 5.9 0.9 - - - +
736A LEU* 6.1 0.2 - - - +
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Residues in contact with SER 404 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
400A LYS 3.1 2.0 + - - -
401A GLY 2.6 14.3 + - - -
403A GLN* 1.3 74.8 - - - +
405A GLY* 1.3 53.8 + - - -
406A VAL* 3.2 12.1 + - - +
666A LYS* 3.0 35.2 + - - -
734A VAL* 5.8 2.9 - - - -
736A LEU* 3.0 31.2 - - - +
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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) + - + + + + + -
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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