Contacts of the helix formed by residues 332 - 350 (chain G) in PDB entry 7CR3
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 ARG 332 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326G GLN* 4.6 17.0 + - - +
330G GLU* 2.8 26.7 + - + +
331G LYS* 1.3 76.3 - - - +
333G ARG* 1.3 63.7 + - - +
334G ASN 3.3 2.7 - - - -
335G PRO* 3.3 5.3 - - + +
336G ALA* 3.1 20.6 + - - +
555G PHE* 4.4 6.0 - - + -
558G SER* 3.4 28.3 - - - +
559G LEU* 2.4 54.9 + - + +
561G PRO* 3.4 25.2 + - - +
91H ARG* 4.1 21.1 - - - +
92H VAL* 3.6 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 333 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328G HIS 5.7 1.4 + - - -
330G GLU* 3.4 22.2 + - - +
331G LYS* 3.1 53.3 - - - +
332G ARG* 1.3 77.8 - - - +
334G ASN* 1.3 74.6 + - - +
336G ALA* 4.1 1.3 - - - -
337G ALA* 2.9 27.5 + - - +
92H VAL* 3.7 19.3 - - + +
93H PHE* 3.1 32.3 - - + -
113H LEU* 4.7 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 334 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331G LYS 4.8 6.6 + - - +
333G ARG* 1.3 88.0 - - - +
335G PRO* 1.3 65.0 - - + +
337G ALA 3.4 0.2 + - - -
338G GLY* 3.0 23.9 + - - -
113H LEU* 3.2 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 335 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331G LYS 4.8 2.0 - - - +
332G ARG* 3.3 17.0 - - - +
334G ASN* 1.3 94.5 - - + +
336G ALA* 1.3 55.2 + - - +
338G GLY* 3.7 2.9 - - - +
339G LEU* 2.8 28.1 + - - +
551G SER* 4.6 1.8 + - - +
554G LYS* 4.2 12.8 - - + +
555G PHE* 3.6 36.9 - - + +
558G SER* 3.5 26.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 336 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332G ARG 3.1 18.9 + - - +
333G ARG* 3.4 7.2 - - - +
334G ASN 3.2 0.2 - - - -
335G PRO* 1.3 74.1 - - - +
337G ALA* 1.3 65.7 + - - +
339G LEU* 3.0 12.8 + - - +
340G ILE* 3.1 18.7 + - - +
555G PHE* 3.6 13.6 - - + -
89H ALA* 3.5 34.0 - - - +
92H VAL* 4.2 5.2 - - + -
93H PHE* 3.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 337 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333G ARG 2.9 6.3 + - - -
336G ALA* 1.3 75.4 - - - +
338G GLY* 1.3 57.7 + - - +
340G ILE* 3.4 7.2 + - - +
341G GLN* 2.8 40.2 + - - +
93H PHE* 3.2 26.5 - - + -
109H VAL* 4.6 5.8 - - + +
110H MET* 4.1 6.8 - - + +
113H LEU* 3.6 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 338 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334G ASN 3.0 15.5 + - - -
335G PRO* 3.7 4.5 - - - -
337G ALA* 1.3 75.8 - - - +
339G LEU* 1.3 64.4 + - - +
341G GLN* 3.2 15.9 + - - +
342G SER* 3.0 22.3 + - - -
551G SER* 3.2 13.8 + - - -
113H LEU* 5.0 0.4 - - - +
114H GLY* 6.2 0.7 - - - -
115H GLU* 5.5 2.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 339 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335G PRO 2.8 16.5 + - - +
336G ALA* 3.0 11.2 + - - +
338G GLY* 1.3 74.1 - - - +
340G ILE* 1.3 59.4 + - - +
343G ALA* 2.9 31.8 + - + +
548G PHE* 3.4 10.7 - - + -
551G SER* 3.2 11.8 + - - +
552G LYS* 3.5 45.5 - - + -
555G PHE* 4.0 15.9 - - + -
85H GLU* 3.8 20.4 - - + +
86H ILE* 3.9 17.5 - - + +
89H ALA* 3.6 23.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 340 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336G ALA 3.1 16.0 + - - +
337G ALA* 4.0 3.4 - - - +
339G LEU* 1.3 75.3 - - + +
341G GLN* 1.3 63.5 + - - +
343G ALA* 3.6 6.9 - - + +
344G TRP* 3.0 24.7 + - + +
86H ILE* 4.9 7.6 - - + -
89H ALA* 4.5 18.8 - - + +
90H PHE* 3.7 52.0 - - + +
93H PHE* 4.7 9.2 - - + -
110H MET* 3.6 27.8 - - + -
125H MET* 4.7 3.9 - - + +
142H PHE* 5.5 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 341 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337G ALA 2.8 19.9 + - - +
338G GLY* 3.2 20.9 + - - +
339G LEU 3.2 0.2 - - - -
340G ILE* 1.3 78.8 - - - +
342G SER* 1.3 59.4 + - - +
344G TRP* 3.2 3.8 + - - +
345G ARG* 3.0 30.8 + - - +
110H MET* 2.9 40.5 + - + +
113H LEU* 2.3 30.0 + - - +
114H GLY* 4.4 0.7 - - - -
115H GLU* 3.0 47.5 + - + +
116H LYS* 4.9 0.9 - - - -
117H LEU* 4.7 4.1 - - + +
125H MET* 4.6 6.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 342 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338G GLY 3.0 12.5 + - - -
341G GLN* 1.3 76.6 - - - +
343G ALA* 1.3 59.3 + - - +
345G ARG* 3.4 19.3 - - - +
346G PHE* 2.9 28.2 + - - +
544G CYS 3.7 4.5 + - - -
547G ARG* 3.5 11.8 - - - +
548G PHE* 3.1 40.0 + - - +
551G SER* 4.3 3.4 - - - -
115H GLU* 6.2 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 343 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339G LEU 2.9 20.8 + - - +
340G ILE* 3.6 9.6 - - + +
341G GLN 3.2 0.2 - - - -
342G SER* 1.3 76.8 - - - +
344G TRP* 1.3 56.8 + - - +
346G PHE* 3.2 2.3 + - - +
347G TYR* 3.0 23.6 + - - +
548G PHE* 3.5 27.5 - - + -
77H MET* 3.6 19.3 - - + +
86H ILE* 4.5 15.5 - - + -
146H MET* 5.9 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 344 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340G ILE* 3.0 14.2 + - + +
341G GLN 3.7 0.2 - - - +
343G ALA* 1.3 73.0 - - - +
345G ARG* 1.3 60.7 + - - +
347G TYR* 3.4 33.2 - + - +
348G ALA* 2.8 37.9 + - + +
356G LEU* 5.7 5.4 - - + -
359G THR* 3.9 20.5 + - - -
117H LEU* 4.4 4.9 - - + -
121H GLU* 3.6 11.2 + - - +
124H GLU* 3.5 34.5 - - + +
125H MET* 3.5 48.5 - - + -
128H GLU* 3.5 37.9 - - + -
142H PHE* 3.9 19.3 - + - -
146H MET* 4.5 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 345 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341G GLN 3.0 17.6 + - - +
342G SER* 3.4 24.5 - - - +
343G ALA 3.2 0.2 - - - -
344G TRP* 1.3 77.2 - - - +
346G PHE* 1.3 50.9 + - - +
348G ALA* 3.9 3.4 - - - +
349G THR* 2.4 41.9 + - - +
359G THR* 4.8 5.6 - - + -
362G TYR* 4.5 5.3 + - - -
363G TYR* 2.7 33.3 + - + +
544G CYS* 3.3 12.8 - - - -
547G ARG* 3.0 35.7 - - - +
115H GLU* 3.2 46.5 + - - +
116H LYS 4.3 5.1 + - - -
117H LEU* 3.9 30.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 346 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
342G SER 2.9 13.4 + - - +
343G ALA 3.2 5.4 + - - +
345G ARG* 1.3 73.9 - - - +
347G TYR* 1.3 53.0 + - - +
349G THR* 2.8 8.7 + - - -
350G ASN* 2.6 64.0 + - + +
544G CYS* 3.4 8.3 - - - -
545G VAL* 3.7 30.5 - - + -
548G PHE* 4.3 22.2 - + + -
73H MET* 6.4 0.4 - - + -
75H ARG 4.5 12.3 - - - -
76H LYS* 3.6 22.0 - - + -
77H MET* 3.6 44.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 347 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343G ALA 3.0 16.0 + - - +
344G TRP* 3.4 38.6 - + - +
346G PHE* 1.3 79.5 - - - +
348G ALA* 1.3 64.8 + - - +
350G ASN* 3.1 20.3 + - + +
352G SER* 4.5 16.8 + - - -
353G ARG* 2.8 43.2 + - + +
356G LEU* 3.4 23.8 - - + +
76H LYS* 4.9 13.2 - - - -
77H MET* 4.0 7.6 - - + -
128H GLU* 3.3 7.5 + - + -
145H MET* 5.6 0.7 - - - -
146H MET* 3.4 41.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 348 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344G TRP* 2.8 35.4 + - + +
347G TYR* 1.3 76.2 - - - +
349G THR* 1.3 52.0 + - - +
356G LEU* 3.3 21.9 - - + +
359G THR* 3.7 33.4 - - + +
360G TRP* 2.4 34.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 349 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345G ARG 2.4 25.6 + - - +
346G PHE* 2.8 17.8 + - - -
348G ALA* 1.3 73.1 - - - +
350G ASN* 1.3 56.5 + - - +
359G THR* 5.0 3.1 - - + -
360G TRP* 3.0 21.3 - - + -
363G TYR* 4.5 14.6 - - + -
540G ILE* 4.4 22.7 - - + -
541G ARG* 2.3 55.4 + - + +
544G CYS* 3.6 11.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 350 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346G PHE* 2.6 43.4 + - + +
347G TYR* 3.1 15.1 + - + +
348G ALA 4.0 0.2 - - - +
349G THR* 1.3 78.5 - - - +
351G LEU* 1.3 72.2 + - - +
352G SER* 3.1 32.8 + - - +
353G ARG 4.2 1.2 - - - +
356G LEU* 3.5 19.6 - - - +
360G TRP* 4.7 0.9 - - - -
541G ARG* 3.9 3.1 + - - +
76H LYS* 3.1 39.3 - - - +
----------------------------------------------------------
Back to top of page
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