Contacts of the helix formed by residues 316 - 331 (chain A) in PDB entry 5M64
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 LEU 316 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86A TYR* 4.8 0.2 - - - -
314A TYR 4.1 2.5 - - - +
315A ILE* 1.3 89.4 - - - +
317A SER* 1.3 63.0 + - - +
318A THR* 3.2 27.4 - - + +
319A GLU* 3.4 36.4 + - + +
320A VAL* 3.8 5.5 + - - +
427A PHE* 5.6 14.6 - - + -
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Residues in contact with SER 317 (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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83A VAL* 4.2 24.9 - - - +
84A PRO* 3.1 33.1 + - - +
85A CYS* 5.1 0.7 - - - -
86A TYR* 4.7 11.5 + - - -
315A ILE 5.3 0.2 + - - -
316A LEU* 1.3 73.3 - - - +
318A THR* 1.3 61.7 + - - +
320A VAL* 3.3 11.8 - - - +
321A LYS* 2.9 27.8 + - - +
356A PHE* 5.0 2.5 - - - -
431A GLN* 5.7 1.9 + - - -
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Residues in contact with THR 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A VAL* 5.1 10.3 - - + -
84A PRO* 5.0 11.7 - - + -
316A LEU* 3.2 21.8 - - + +
317A SER* 1.3 77.4 - - - +
319A GLU* 1.3 61.8 + - - +
321A LYS* 3.4 9.9 - - + +
322A ASN* 2.9 40.8 + - - +
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Residues in contact with GLU 319 (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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314A TYR 5.3 0.2 - - - +
315A ILE* 3.7 28.9 - - + +
316A LEU* 3.4 34.0 + - + +
317A SER 3.2 0.8 - - - -
318A THR* 1.3 81.5 + - - +
320A VAL* 1.3 58.6 + - - +
322A ASN* 3.2 8.5 + - - +
323A ILE* 3.0 46.5 + - + +
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Residues in contact with VAL 320 (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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86A TYR* 3.8 21.3 - - + +
98A LEU* 4.1 23.3 - - + -
243A PHE* 5.7 2.2 - - + -
251A ILE* 6.1 2.2 - - + -
315A ILE* 3.7 25.4 - - + -
316A LEU 3.8 4.3 - - - +
317A SER* 3.3 16.2 - - - +
319A GLU* 1.3 73.8 - - - +
321A LYS* 1.3 59.8 + - - +
323A ILE* 3.7 13.5 - - + -
324A LEU* 3.0 39.4 + - + +
356A PHE* 3.9 23.0 - - + -
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Residues in contact with LYS 321 (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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84A PRO* 3.8 28.5 - - + +
317A SER 2.9 19.7 + - - +
318A THR* 3.4 13.2 - - + +
319A GLU 3.1 0.4 - - - -
320A VAL* 1.3 77.9 - - - +
322A ASN* 1.3 63.6 + - - +
324A LEU* 4.2 0.5 - - - +
325A ASP* 2.9 35.9 + - + +
352A ALA* 4.0 8.0 + - + -
353A ASP* 2.6 32.4 + - - +
356A PHE* 3.3 39.9 - - - +
358A ASP* 4.7 1.4 + - - -
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Residues in contact with ASN 322 (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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318A THR* 2.9 28.2 + - - +
319A GLU* 3.2 5.6 + - - +
321A LYS* 1.3 79.7 - - - +
323A ILE* 1.3 56.6 + - + +
325A ASP* 3.8 7.5 + - - +
326A THR* 2.7 43.7 + - + +
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Residues in contact with ILE 323 (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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98A LEU* 5.1 8.5 - - + -
101A SER* 4.8 9.9 - - - +
102A CYS 5.3 4.7 - - - +
103A LEU* 5.8 11.7 - - + -
106A HIS* 5.8 8.5 - - + +
243A PHE* 5.7 8.5 - - + -
319A GLU* 3.0 40.3 + - + +
320A VAL* 3.8 14.6 - - + +
321A LYS 3.3 0.2 - - - -
322A ASN* 1.3 77.5 - - + +
324A LEU* 1.3 69.0 + - + +
326A THR* 2.7 20.8 + - - -
327A VAL* 3.0 31.6 + - + +
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Residues in contact with LEU 324 (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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94A LEU* 4.5 15.5 - - + +
97A TYR* 4.9 17.9 - - + +
98A LEU* 4.1 27.4 - - + -
101A SER* 6.1 0.7 - - - -
320A VAL* 3.0 32.2 + - + +
323A ILE* 1.3 83.9 - - + +
325A ASP* 1.3 62.4 + - - +
327A VAL* 3.7 10.8 - - + -
328A PHE* 3.1 63.2 + - + -
352A ALA* 3.9 17.5 - - + -
356A PHE* 4.3 15.5 - - + -
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Residues in contact with ASP 325 (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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321A LYS* 2.9 27.6 + - + +
322A ASN* 3.8 9.8 + - - +
323A ILE 3.2 0.2 - - - -
324A LEU* 1.3 75.8 - - - +
326A THR* 1.3 62.5 + - - +
328A PHE* 4.4 2.0 - - - +
329A ARG* 2.4 63.4 + - - +
351A LYS* 3.8 19.8 + - - -
352A ALA* 3.8 15.1 + - + +
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Residues in contact with THR 326 (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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106A HIS* 4.0 29.7 + - + +
322A ASN* 2.7 19.9 + - + +
323A ILE* 2.7 23.0 + - - -
325A ASP* 1.3 78.0 - - - +
327A VAL* 1.3 60.4 + - - +
328A PHE 3.2 1.6 - - - -
329A ARG* 3.4 19.8 + - - +
330A LYS* 3.0 31.1 + - - +
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Residues in contact with VAL 327 (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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97A TYR* 6.3 0.9 - - + -
101A SER* 3.3 30.1 - - - +
102A CYS 4.9 0.7 - - - +
106A HIS* 3.3 28.9 - - + +
108A PHE* 6.1 3.1 - - + -
323A ILE* 3.0 26.6 + - + +
324A LEU* 3.7 26.7 - - + +
326A THR* 1.3 79.3 - - - +
328A PHE* 1.3 65.7 + - + +
330A LYS* 3.7 7.6 - - - -
331A GLU* 3.0 38.0 + - - +
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Residues in contact with PHE 328 (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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94A LEU* 5.6 0.9 - - + -
97A TYR* 5.4 11.7 - + + -
324A LEU* 3.1 49.9 + - + +
325A ASP* 4.4 3.6 - - - +
326A THR 3.2 0.2 - - - -
327A VAL* 1.3 84.4 - - + +
329A ARG* 1.3 62.6 + - + +
331A GLU 3.6 0.9 - - - -
332A GLN* 2.8 35.3 + - - +
335A LEU* 3.5 41.0 - - + +
339A PHE* 4.9 1.8 - + - -
350A VAL 4.9 4.9 - - - +
351A LYS* 3.7 9.4 - - - -
352A ALA* 3.5 37.0 - - + +
354A SER* 5.0 0.4 - - - -
355A PHE* 4.2 27.8 - + - -
356A PHE* 6.3 0.2 - + - -
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Residues in contact with ARG 329 (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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325A ASP* 2.4 54.8 + - - +
326A THR* 3.4 17.4 + - - +
328A PHE* 1.3 77.8 - - + +
330A LYS* 1.3 57.8 + - - +
332A GLN* 4.0 15.5 + - - +
349A LEU* 5.9 11.9 - - + -
351A LYS* 5.5 5.6 - - - +
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Residues in contact with LYS 330 (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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105A CYS 2.8 24.2 + - - -
106A HIS* 3.4 35.3 + - + +
107A HIS* 3.3 33.9 + - + -
326A THR* 3.0 17.0 + - - +
327A VAL* 3.9 6.7 - - - +
328A PHE 3.1 0.4 - - - -
329A ARG* 1.3 79.8 - - - +
331A GLU* 1.3 60.4 + - + +
332A GLN 3.5 1.3 + - - -
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Residues in contact with GLU 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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106A HIS 4.8 1.6 - - - -
107A HIS* 3.2 19.4 + - - +
108A PHE* 2.5 74.8 + - - +
115A VAL* 5.4 4.7 - - + +
327A VAL* 3.0 20.8 + - - +
328A PHE 3.6 3.4 - - - -
330A LYS* 1.3 82.2 - - + +
332A GLN* 1.3 59.4 + - - +
333A CYS* 3.2 5.1 + - - +
334A VAL* 3.3 14.0 - - + +
335A LEU* 2.9 27.1 + - + +
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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