Contacts of the helix formed by residues 361 - 375 (chain B) in PDB entry 3LRB
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 THR 361 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B LEU 5.1 0.2 - - - -
93B TYR* 4.4 20.0 - - + -
96B ALA* 4.1 14.1 - - + +
205B ILE* 3.6 21.4 - - + +
208B GLU* 4.6 1.7 - - - +
293B TRP* 5.0 4.7 - - + -
357B SER 3.0 23.6 - - - +
358B VAL* 2.9 15.2 + - + +
360B PHE* 1.3 75.5 - - - +
362B LEU* 1.3 59.0 + - - +
364B PRO* 3.1 21.7 - - - +
365B TYR* 2.9 37.1 + - - -
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PHE* 6.2 0.7 - - + -
418A MET* 5.1 4.7 - - + -
205B ILE* 5.8 4.5 - - + -
358B VAL* 3.8 11.7 - - + +
359B ILE* 2.9 34.0 + - + +
360B PHE 2.9 1.6 + - - -
361B THR* 1.3 77.7 + - - +
363B VAL* 1.3 52.3 - - + +
364B PRO 3.1 2.2 - - - -
365B TYR* 2.5 44.8 + - + +
366B LEU* 2.6 20.4 + - - +
397B TYR* 5.5 8.1 - - + -
398B CYS* 4.0 31.3 - - + +
401B ALA* 4.6 14.8 - - + -
402B VAL* 4.1 20.2 - - + +
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Residues in contact with VAL 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414A PHE* 4.0 28.0 - - + -
418A MET* 5.9 2.9 - - + +
88B GLN* 4.2 9.0 - - - +
89B THR* 5.1 2.9 - - - -
92B LEU* 3.4 28.9 - - + -
359B ILE 4.8 2.7 - - - +
360B PHE* 3.2 4.0 + - - +
362B LEU* 1.3 75.4 - - + +
364B PRO* 1.3 68.1 - - + +
366B LEU* 3.4 8.6 + - + +
367B TYR* 3.1 53.3 + - + +
417B LEU* 4.3 9.4 - - + -
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Residues in contact with PRO 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TYR* 3.9 3.1 - - - +
73B SER* 3.2 21.1 + - - +
89B THR* 3.5 35.2 - - - +
92B LEU* 3.4 5.4 - - + -
93B TYR* 4.0 19.7 - - + -
208B GLU* 4.9 2.2 - - - +
360B PHE 3.0 26.7 - - - +
361B THR* 3.1 13.7 - - - +
363B VAL* 1.3 79.5 - - + +
365B TYR* 1.3 58.9 + - - +
367B TYR* 3.8 1.4 - - + +
368B THR* 2.9 32.1 + - - -
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Residues in contact with TYR 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 3.2 20.5 - - + +
60B TYR* 3.4 25.6 - + - -
205B ILE* 4.2 8.3 - - + -
206B GLY* 2.8 33.4 + - - -
207B VAL* 3.4 24.1 + - + -
208B GLU* 3.3 25.1 + - - +
361B THR* 2.9 41.7 + - - -
362B LEU* 2.5 26.4 + - + +
364B PRO* 1.3 72.8 - - - +
366B LEU* 1.3 62.3 + - - +
368B THR* 3.1 4.0 + - - -
369B CYS* 3.1 26.9 + - - -
398B CYS* 3.3 20.0 - - - -
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418A MET* 3.5 44.4 - - + +
421A THR* 3.4 35.7 - - + +
362B LEU 2.6 14.3 + - - +
363B VAL* 3.6 13.7 - - - +
365B TYR* 1.3 73.1 - - - +
367B TYR* 1.3 61.5 + - + +
369B CYS* 3.3 7.2 + - - +
370B ALA* 3.1 22.3 + - - +
395B PHE* 3.8 25.2 - - + +
398B CYS* 3.7 24.3 - - + -
399B ILE* 4.5 5.4 - - + -
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Residues in contact with TYR 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 4.1 27.5 - + - -
85A LEU* 5.6 0.2 - - - +
88A GLN* 5.3 1.4 + - - -
421A THR* 4.5 12.3 - - + -
73B SER 5.5 0.4 - - - +
76B TYR* 4.9 1.5 - - - +
77B ALA* 4.1 19.6 + - + -
80B CYS* 4.7 13.8 - - + +
85B LEU* 3.3 32.4 - - + +
88B GLN* 3.2 27.1 + - - -
89B THR* 4.0 18.6 - - - +
363B VAL* 3.1 35.1 + - + +
364B PRO 4.0 2.9 - - - +
366B LEU* 1.3 79.6 - - + +
368B THR* 1.3 66.9 + - - +
369B CYS 3.1 1.3 - - - -
370B ALA* 3.5 4.6 - - + +
371B ALA* 2.9 26.5 + - - +
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Residues in contact with THR 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B VAL* 3.7 14.4 - - + -
60B TYR* 2.5 62.5 + - + -
63B MET* 4.7 4.8 - - + +
73B SER* 3.6 12.4 + - - -
76B TYR* 3.8 14.5 - - + -
364B PRO 2.9 16.6 + - - -
365B TYR 3.1 6.0 + - - +
367B TYR* 1.3 76.5 - - - +
369B CYS* 1.3 59.9 + - - +
371B ALA* 3.7 5.2 - - - +
372B LEU* 2.9 27.0 + - - +
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Residues in contact with CYS 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B LEU* 4.0 13.7 - - - -
59B VAL* 3.9 14.1 - - - -
365B TYR 3.1 16.8 + - - -
366B LEU 3.4 9.0 - - - +
368B THR* 1.3 74.9 - - - +
370B ALA* 1.3 66.4 + - - +
372B LEU* 3.2 10.0 + - - +
373B LEU* 3.6 17.7 + - - +
391B THR* 4.7 1.8 - - - +
394B ALA* 3.4 39.9 - - - -
395B PHE* 3.7 24.5 - - + -
398B CYS* 4.5 4.0 - - - -
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Residues in contact with ALA 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A PHE* 5.9 0.4 - - + -
421A THR* 4.5 16.6 - - + +
424A TYR* 5.6 4.3 - - + +
80B CYS* 4.0 24.0 - - - -
366B LEU 3.1 13.5 + - - +
367B TYR* 3.2 11.2 + - - +
369B CYS* 1.3 75.3 - - - +
371B ALA* 1.3 62.8 + - - +
373B LEU* 3.0 9.9 + - - +
374B LEU* 2.9 31.7 - - + +
395B PHE* 3.8 10.2 - - + -
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Residues in contact with ALA 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B MET* 3.7 8.3 - - + -
76B TYR* 3.5 43.3 - - + +
79B ARG 5.2 0.4 - - - -
80B CYS* 4.7 7.5 - - + +
367B TYR 2.9 16.8 + - - +
368B THR 3.7 1.8 - - - +
370B ALA* 1.3 71.5 - - - +
372B LEU* 1.3 54.5 + - - +
373B LEU 2.4 19.2 + - - -
374B LEU* 4.5 2.9 - - - +
375B LEU* 3.0 33.5 + - + +
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Residues in contact with LEU 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B MET 4.8 0.9 - - - +
59B VAL* 3.3 44.6 - - + +
62B LYS* 4.0 25.1 - - + +
63B MET* 3.8 22.2 - - + +
66B LEU* 4.5 9.4 - - + -
368B THR 2.9 17.1 + - - +
369B CYS* 3.2 7.5 + - - +
371B ALA* 1.3 72.0 - - - +
373B LEU* 1.3 65.2 + - - +
376B GLY 4.6 3.3 + - - +
379B HIS* 3.5 19.6 + - + +
387B TYR* 5.9 6.7 - - + -
390B VAL* 5.6 1.8 - - + -
391B THR* 3.4 20.2 - - + -
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Residues in contact with LEU 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
428A TYR* 2.6 67.3 - - + +
369B CYS 3.6 17.5 - - - +
370B ALA 3.0 3.8 + - - +
371B ALA 2.4 7.5 + - - -
372B LEU* 1.3 81.6 - - - +
374B LEU* 1.3 51.8 + - - +
375B LEU 2.5 15.7 + - - -
376B GLY 2.7 24.6 + - - +
377B HIS* 3.2 2.1 + - - +
379B HIS* 3.8 18.8 - - + +
384B ARG* 6.2 0.4 - - - +
388B LEU* 4.5 12.8 - - + +
391B THR* 3.0 28.7 - - + +
395B PHE* 4.1 5.4 - - + -
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Residues in contact with LEU 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A TYR* 3.9 23.8 - - + +
427A ASN 4.9 2.0 - - - +
428A TYR* 4.1 17.9 - - + -
429A ASN* 4.8 4.0 - - - +
430A ARG* 2.9 63.0 - - + +
431A LEU 4.4 1.7 + - - +
79B ARG 4.7 9.4 - - - +
80B CYS* 5.5 7.4 - - + -
370B ALA* 2.9 39.3 + - + +
371B ALA* 5.1 0.7 - - - -
373B LEU* 1.3 69.9 - - - +
375B LEU* 1.3 72.9 + - + +
377B HIS* 3.2 24.8 + - - +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431A LEU 4.0 9.0 - - - +
434A ASN* 4.2 5.2 - - + -
435A PRO* 4.1 29.2 - - + +
63B MET* 3.4 30.5 - - + -
66B LEU* 5.0 7.8 - - + +
76B TYR* 4.4 1.6 - - - +
79B ARG* 3.2 59.2 - - + +
371B ALA* 3.0 19.2 + - + +
373B LEU 2.5 6.1 + - - -
374B LEU* 1.3 96.2 - - - +
376B GLY* 1.3 54.3 + - - +
377B HIS* 2.8 13.1 + - - +
380B PHE* 4.1 19.4 - - - -
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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