Contacts of the helix formed by residues 330 - 344 (chain A) in PDB entry 4R54
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 330 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A VAL* 4.1 16.6 - - + -
94A ASN* 3.5 29.8 - - - +
125A CYS* 3.8 4.3 - - - -
325A ASN 3.4 12.3 + - - +
326A LEU* 3.8 4.5 - - - +
327A LEU 2.9 6.1 + - - -
328A LYS 3.1 1.4 + - - -
329A GLY* 1.3 81.0 - - - +
331A ALA* 1.3 61.0 + - - +
333A ASN 3.4 1.3 + - - -
334A SER* 3.0 34.6 + - - -
403A NAP 4.1 5.8 - - + +
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Residues in contact with ALA 331 (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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14A VAL* 4.1 3.1 - - + +
17A GLN* 3.5 15.9 - - + +
18A MET* 3.5 46.4 - - + +
21A MET* 4.0 4.3 - - + -
326A LEU 2.8 21.9 + - - +
327A LEU* 4.7 0.2 - - - -
330A ALA* 1.3 72.5 - - - +
332A TRP* 1.3 57.7 + - - +
334A SER* 3.3 2.1 + - - -
335A VAL* 2.9 34.1 + - - +
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Residues in contact with TRP 332 (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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21A MET* 3.8 23.5 - - + +
25A SER* 6.3 0.9 - - - -
110A GLU* 5.0 2.0 + - - -
300A ARG* 3.5 57.6 + - + +
327A LEU* 2.8 24.6 + - + +
328A LYS* 3.7 25.8 - - + +
331A ALA* 1.3 72.3 - - - +
333A ASN* 1.3 58.4 + - - +
335A VAL* 4.5 8.3 - - + -
336A GLN* 2.7 74.0 + - + +
339A GLU* 3.8 28.7 - - - -
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Residues in contact with ASN 333 (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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107A VAL 3.0 24.2 + - - -
108A VAL* 3.7 5.3 - - - +
109A PRO* 3.3 11.5 - - - +
125A CYS* 3.4 27.6 - - - -
126A PRO* 3.7 5.7 - - - +
131A ILE* 4.0 7.2 - - + -
327A LEU 3.3 5.3 + - - -
328A LYS* 2.9 48.3 + - - +
330A ALA 3.4 1.5 + - - +
332A TRP* 1.3 78.4 - - - +
334A SER* 1.3 56.9 + - - +
336A GLN* 3.4 7.5 + - - +
337A ILE* 2.9 38.4 + - - +
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Residues in contact with SER 334 (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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18A MET* 3.7 20.1 - - - +
69A LEU* 4.4 10.3 - - - +
92A VAL* 3.9 23.5 + - - +
94A ASN* 3.6 16.5 + - - +
125A CYS* 3.7 9.7 - - - +
330A ALA 3.0 20.7 + - - -
331A ALA 3.6 4.5 - - - -
332A TRP 3.2 0.2 - - - -
333A ASN* 1.3 73.5 - - - +
335A VAL* 1.3 66.4 + - - +
337A ILE* 3.1 8.2 + - - +
338A ALA* 3.0 20.4 + - - +
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Residues in contact with VAL 335 (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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18A MET* 4.3 4.3 - - - +
21A MET* 3.7 33.2 - - + +
22A LEU* 4.0 16.4 - - + -
25A SER* 3.8 24.7 - - - +
27A LEU* 5.4 0.4 - - + -
69A LEU* 3.9 22.7 - - + -
331A ALA 2.9 20.3 + - - +
332A TRP* 4.0 8.1 - - + +
334A SER* 1.3 75.9 - - - +
336A GLN* 1.3 58.5 + - - +
338A ALA* 3.1 7.9 + - + +
339A GLU* 2.8 34.4 + - + +
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Residues in contact with GLN 336 (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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109A PRO* 3.8 20.7 - - + +
110A GLU* 3.0 25.6 + - - +
328A LYS* 2.7 29.1 + - - -
332A TRP* 2.7 59.2 + - + +
333A ASN* 3.6 3.4 - - - +
335A VAL* 1.3 74.5 - - - +
337A ILE* 1.3 51.5 + - - +
339A GLU* 3.4 7.3 + - + +
340A THR* 2.7 39.9 + - - +
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Residues in contact with ILE 337 (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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92A VAL* 4.0 21.5 - - + -
107A VAL* 3.5 27.4 - - + +
109A PRO* 4.0 17.3 - - + -
116A LEU* 4.1 8.3 - - + -
123A ILE* 3.7 31.2 - - + -
125A CYS* 4.2 11.7 - - + -
333A ASN* 2.9 27.8 + - - +
334A SER 3.1 6.9 + - - +
336A GLN* 1.3 75.6 - - - +
338A ALA* 1.3 57.7 + - - +
340A THR* 3.0 5.7 + - - -
341A LEU* 2.8 43.1 + - + +
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Residues in contact with ALA 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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22A LEU* 5.9 0.2 - - + -
27A LEU* 3.8 24.9 - - + +
67A ILE* 4.5 20.3 - - + +
69A LEU* 4.5 9.0 - - + -
92A VAL* 4.6 1.3 - - + +
334A SER 3.0 12.2 + - - +
335A VAL* 3.1 11.9 + - - +
337A ILE* 1.3 77.6 - - - +
339A GLU* 1.3 62.7 + - - +
341A LEU* 3.2 14.1 + - - +
342A HIS* 3.0 23.4 + - - +
347A VAL* 4.8 1.7 - - - +
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Residues in contact with GLU 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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25A SER* 2.5 34.7 + - - +
26A THR* 3.1 26.9 + - - +
27A LEU* 3.9 14.4 - - + -
332A TRP* 3.8 25.5 - - - -
335A VAL* 2.8 27.4 + - + +
336A GLN* 3.7 6.9 - - + +
338A ALA* 1.3 72.2 - - - +
340A THR* 1.3 58.0 + - - +
342A HIS* 3.3 4.6 + - + +
343A GLU* 2.9 47.9 + - - +
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Residues in contact with THR 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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109A PRO* 3.9 14.6 - - + +
113A ALA* 4.3 8.3 - - + -
116A LEU* 3.5 24.5 - - + -
336A GLN* 2.7 25.5 + - - +
337A ILE* 3.0 5.8 + - - -
339A GLU* 1.3 75.2 - - - +
341A LEU* 1.3 64.6 + - - +
343A GLU* 3.4 13.0 + - - +
344A ARG* 3.1 57.8 + - - +
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Residues in contact with LEU 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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67A ILE* 5.9 3.1 - - + -
90A VAL* 4.0 22.2 - - + -
92A VAL* 4.0 11.0 - - + -
116A LEU* 4.1 19.7 - - + +
119A HIS* 4.0 18.6 - - + +
123A ILE* 4.0 8.1 - - + -
337A ILE* 2.8 37.9 + - + +
338A ALA* 3.2 10.3 + - + +
340A THR* 1.3 72.2 - - - +
342A HIS* 1.3 61.9 + - - +
344A ARG 3.4 0.9 + - - -
345A GLY 3.2 3.5 + - - -
346A LEU* 2.9 54.2 + - + +
347A VAL* 3.8 15.7 + - + -
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Residues in contact with HIS 342 (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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3A TYR* 2.8 36.4 + + + +
26A THR* 5.3 5.7 + - - -
27A LEU* 3.6 17.5 - - + -
28A PRO* 4.0 28.3 - - + +
338A ALA 3.0 12.3 + - - +
339A GLU* 3.5 8.1 - - + +
341A LEU* 1.3 74.6 - - - +
343A GLU* 1.3 77.3 + - + +
345A GLY* 3.1 13.9 + - - -
347A VAL* 3.7 4.6 - - + +
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Residues in contact with GLU 343 (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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26A THR* 4.5 7.6 + - - -
339A GLU* 2.9 37.2 + - - +
340A THR* 3.8 14.7 + - - +
341A LEU 3.3 0.2 - - - -
342A HIS* 1.3 90.6 - - + +
344A ARG* 1.3 59.9 + - + +
402A NA 2.3 29.2 - - - -
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Residues in contact with ARG 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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113A ALA* 3.6 39.9 + - - +
114A HIS* 4.2 6.1 - - - +
116A LEU* 5.4 0.2 - - - -
117A ASP* 4.5 13.8 + - - +
340A THR* 3.1 33.7 + - - +
342A HIS 3.2 0.4 - - - -
343A GLU* 1.3 82.1 + - + +
345A GLY* 1.3 62.9 + - - +
346A LEU* 3.3 26.9 + - + +
402A NA 4.3 2.7 - - - -
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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
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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