Contacts of the helix formed by residues 332 - 350 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A GLN* 4.6 16.2 + - - +
330A GLU* 2.8 27.0 + - + +
331A LYS* 1.3 77.8 - - - +
333A ARG* 1.3 62.9 + - - +
334A ASN 3.3 2.7 - - - -
335A PRO* 3.3 4.7 - - + +
336A ALA* 3.1 20.6 + - - +
555A PHE* 4.4 5.6 - - + -
558A SER* 3.4 29.4 - - - +
559A LEU* 2.4 55.5 + - - +
561A PRO* 3.4 24.4 + - - +
88F GLU* 5.8 0.2 + - - -
91F ARG* 4.1 22.0 - - - +
92F VAL* 3.6 20.0 - - + -
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Residues in contact with ARG 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A HIS 5.7 1.4 + - - -
330A GLU* 3.4 22.6 + - - +
331A LYS* 3.1 54.0 - - - +
332A ARG* 1.3 77.7 - - - +
334A ASN* 1.3 74.8 + - - +
336A ALA* 3.2 1.5 + - - -
337A ALA* 2.9 26.9 + - - +
92F VAL* 3.7 19.2 - - + +
93F PHE* 3.1 32.9 - - + -
113F LEU* 4.7 4.3 - - + -
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Residues in contact with ASN 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LYS 4.8 6.3 + - - -
332A ARG* 4.4 0.2 - - - +
333A ARG* 1.3 86.2 - - - +
335A PRO* 1.3 66.8 - - + +
337A ALA 3.4 0.2 + - - -
338A GLY* 3.0 23.4 + - - -
113F LEU* 3.2 33.7 - - + +
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Residues in contact with PRO 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A LYS 4.8 2.0 - - - +
332A ARG* 3.3 17.3 - - - +
334A ASN* 1.3 95.0 - - + +
336A ALA* 1.3 54.5 + - - +
338A GLY* 3.7 2.8 - - - +
339A LEU* 2.8 28.4 + - - +
551A SER* 4.6 2.2 + - - +
554A LYS* 4.2 13.5 - - + +
555A PHE* 3.6 37.8 - - + +
558A SER* 3.5 27.1 - - - +
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Residues in contact with ALA 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332A ARG 3.1 19.9 + - - +
333A ARG* 3.4 7.0 - - - +
334A ASN 3.2 0.6 - - - -
335A PRO* 1.3 73.5 - - - +
337A ALA* 1.3 66.2 + - - +
339A LEU* 3.0 13.0 + - - +
340A ILE* 3.1 18.7 + - - +
555A PHE* 3.6 13.2 - - + -
89F ALA* 3.5 34.9 - - - +
92F VAL* 4.2 5.2 - - + -
93F PHE* 3.7 7.4 - - + -
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Residues in contact with ALA 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ARG 2.9 5.9 + - - -
336A ALA* 1.3 75.6 - - - +
338A GLY* 1.3 57.4 + - - +
340A ILE* 3.4 7.7 + - - +
341A GLN* 2.8 39.5 + - - +
93F PHE* 3.2 27.7 - - + -
109F VAL* 4.6 5.4 - - + +
110F MET* 4.1 6.3 - - + +
113F LEU* 3.6 31.2 - - + -
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Residues in contact with GLY 338 (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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334A ASN 3.0 15.1 + - - -
335A PRO* 3.8 4.0 - - - -
337A ALA* 1.3 77.0 - - - +
339A LEU* 1.3 62.1 + - - +
341A GLN* 3.2 16.1 + - - +
342A SER* 3.0 22.3 + - - -
551A SER* 3.2 14.2 + - - -
113F LEU* 5.0 0.6 - - - +
114F GLY* 6.2 0.7 - - - -
115F GLU* 5.5 2.6 - - - +
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Residues in contact with LEU 339 (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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335A PRO 2.8 16.1 + - - +
336A ALA* 3.0 11.4 + - - +
338A GLY* 1.3 74.4 - - - +
340A ILE* 1.3 57.6 + - - +
343A ALA* 2.9 31.6 + - + +
548A PHE* 3.4 11.8 - - + -
551A SER* 3.2 12.1 + - - +
552A LYS* 3.5 45.3 - - + -
555A PHE* 4.0 15.5 - - + -
82F SER* 6.5 0.4 - - - -
85F GLU* 3.8 20.0 - - + +
86F ILE* 3.9 17.3 - - + +
89F ALA* 3.6 23.3 - - + -
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Residues in contact with ILE 340 (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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336A ALA 3.1 16.7 + - - +
337A ALA* 4.0 3.1 - - - +
339A LEU* 1.3 75.1 - - + +
341A GLN* 1.3 63.1 + - - +
343A ALA* 3.6 6.9 - - + +
344A TRP* 3.0 25.4 + - + +
86F ILE* 4.9 8.3 - - + -
89F ALA* 4.5 17.9 - - + +
90F PHE* 3.7 51.4 - - + +
93F PHE* 4.7 9.4 - - + -
110F MET* 3.6 27.4 - - + -
125F MET* 4.7 3.9 - - + +
142F PHE* 5.5 7.0 - - + -
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Residues in contact with GLN 341 (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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337A ALA 2.8 21.0 + - - +
338A GLY* 3.2 20.1 + - - +
339A LEU 3.2 0.2 - - - -
340A ILE* 1.3 78.6 - - - +
342A SER* 1.3 59.6 + - - +
344A TRP* 3.2 4.0 + - - +
345A ARG* 3.0 29.4 + - - +
110F MET* 2.9 42.0 + - + +
113F LEU* 2.3 30.3 + - - +
114F GLY* 4.4 0.7 - - - -
115F GLU* 3.0 48.5 + - + +
116F LYS 5.4 0.4 - - - -
117F LEU* 4.7 3.9 - - + +
125F MET* 4.6 5.7 - - + +
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Residues in contact with SER 342 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A GLY 3.0 12.6 + - - -
341A GLN* 1.3 76.8 - - - +
343A ALA* 1.3 60.6 + - - +
345A ARG* 3.4 19.5 - - - +
346A PHE* 2.9 28.1 + - - +
544A CYS* 3.7 5.2 + - - -
547A ARG* 3.5 11.8 - - - +
548A PHE* 3.1 39.9 + - - +
551A SER* 4.3 3.4 - - - -
115F GLU* 6.2 2.5 - - - -
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Residues in contact with ALA 343 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A LEU* 2.9 20.6 + - + +
340A ILE* 3.6 9.6 - - + +
341A GLN 3.2 0.2 - - - -
342A SER* 1.3 77.4 - - - +
344A TRP* 1.3 56.5 + - - +
346A PHE* 3.2 1.9 + - - +
347A TYR* 3.0 23.4 + - - +
548A PHE* 3.5 27.7 - - + -
77F MET* 3.6 20.2 - - + +
86F ILE* 4.5 15.3 - - + -
146F MET* 5.9 0.9 - - - -
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Residues in contact with TRP 344 (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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340A ILE* 3.0 14.0 + - + +
341A GLN 3.7 0.7 - - - +
343A ALA* 1.3 73.8 - - - +
345A ARG* 1.3 60.5 + - - +
347A TYR* 3.4 32.8 - + - +
348A ALA* 2.8 39.1 + - + +
356A LEU* 5.7 5.4 - - + -
359A THR* 3.9 20.2 + - - -
117F LEU* 4.4 4.3 - - + -
121F GLU 3.6 11.4 + - - -
124F GLU* 3.5 32.9 - - + +
125F MET* 3.5 48.9 - - + -
128F GLU* 3.5 38.4 - - + -
142F PHE* 3.9 19.7 - + - -
146F MET* 4.5 2.9 - - + -
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Residues in contact with ARG 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341A GLN 3.0 17.8 + - - +
342A SER* 3.4 25.8 - - - +
343A ALA 3.2 0.2 - - - -
344A TRP* 1.3 77.0 - - - +
346A PHE* 1.3 50.2 + - - +
348A ALA* 3.9 3.4 - - - +
349A THR* 2.4 41.4 + - - +
359A THR* 4.8 6.3 - - + -
362A TYR* 4.5 4.6 + - - -
363A TYR* 2.7 33.3 + - + +
544A CYS* 3.3 13.9 - - - -
547A ARG* 3.0 35.5 - - - +
115F GLU* 3.2 44.3 + - - +
116F LYS 4.3 5.7 + - - -
117F LEU* 3.9 31.4 - - + +
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Residues in contact with PHE 346 (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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342A SER 2.9 13.5 + - - +
343A ALA 3.2 6.0 + - - +
345A ARG* 1.3 73.5 - - - +
347A TYR* 1.3 53.1 + - - +
349A THR* 2.8 8.6 + - - -
350A ASN* 2.6 64.4 + - + +
544A CYS* 3.4 8.5 - - - -
545A VAL* 3.7 31.4 - - + -
548A PHE* 4.3 21.5 - + + -
73F MET* 6.4 0.4 - - + -
75F ARG 4.5 13.0 - - - -
76F LYS* 3.6 22.0 - - + -
77F MET* 3.6 43.7 - - + -
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Residues in contact with TYR 347 (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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343A ALA 3.0 16.0 + - - +
344A TRP* 3.4 37.9 - + - +
346A PHE* 1.3 79.7 - - - +
348A ALA* 1.3 64.3 + - - +
350A ASN* 3.1 19.5 + - + +
352A SER* 4.5 16.6 + - - -
353A ARG* 2.8 42.2 + - + +
356A LEU* 3.4 24.5 - - + +
76F LYS* 4.9 13.7 - - - -
77F MET* 4.0 7.0 - - + -
128F GLU* 3.3 8.6 + - + -
145F MET* 5.6 0.9 - - - -
146F MET* 3.4 42.2 - - + -
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Residues in contact with ALA 348 (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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344A TRP* 2.8 34.7 + - + +
345A ARG 4.1 0.2 - - - +
347A TYR* 1.3 76.8 - - - +
349A THR* 1.3 51.5 + - - +
356A LEU* 3.3 22.3 - - + +
359A THR* 3.7 33.7 - - + +
360A TRP* 2.4 34.5 + - + +
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Residues in contact with THR 349 (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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345A ARG 2.4 26.8 + - - +
346A PHE* 2.8 18.4 + - - -
348A ALA* 1.3 74.2 - - - +
350A ASN* 1.3 56.5 + - - +
359A THR* 5.0 2.7 - - + -
360A TRP* 3.0 21.1 - - + -
363A TYR* 4.5 15.5 - - + -
540A ILE* 4.4 22.4 - - + -
541A ARG* 2.3 56.3 + - + +
544A CYS* 3.6 11.2 - - + +
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Residues in contact with ASN 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346A PHE* 2.6 42.4 + - + +
347A TYR* 3.1 14.6 + - + +
348A ALA 4.0 0.2 - - - +
349A THR* 1.3 77.0 - - - +
351A LEU* 1.3 72.0 + - - +
352A SER* 3.1 33.4 + - - +
353A ARG 4.2 1.2 - - - +
356A LEU* 3.5 19.9 - - - +
360A TRP* 4.7 0.9 - - - -
541A ARG* 3.9 4.0 + - - +
76F LYS* 3.1 39.5 - - - +
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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