Contacts of the helix formed by residues 322 - 333 (chain A) in PDB entry 5NDD
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 VAL 322 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306A LEU* 4.1 18.2 - - + -
309A VAL* 3.7 32.5 - - + -
310A HIS* 4.0 22.9 - - + +
313A LEU* 4.0 2.9 - - + -
320A SER* 4.0 9.0 - - - -
321A HIS* 1.3 97.3 - - + +
323A TYR* 1.3 53.5 + - - +
324A ALA 3.2 3.1 - - - -
325A LEU* 3.1 20.7 + - + -
326A TYR* 2.7 35.9 + - - +
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Residues in contact with TYR 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 3.9 8.3 - - + -
65A SER* 4.0 31.4 - - - +
68A VAL* 3.7 39.9 - - + -
69A LEU* 3.6 23.9 - - + +
228A ASP* 3.1 32.8 + - + +
229A VAL* 4.4 1.0 - - + +
310A HIS* 3.4 24.0 - + - -
320A SER* 3.3 22.4 + - - +
321A HIS 3.1 1.8 - - - -
322A VAL* 1.3 78.5 - - - +
324A ALA* 1.3 61.2 + - - +
326A TYR* 3.4 18.0 - + - +
327A ILE* 3.1 33.1 + - + +
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 4.1 19.5 - - + -
68A VAL* 4.5 12.6 - - + -
73A LEU* 4.2 18.5 - - + +
321A HIS 4.3 1.3 + - - +
322A VAL 3.2 0.2 - - - -
323A TYR* 1.3 76.2 - - - +
325A LEU* 1.3 69.4 + - + +
327A ILE* 3.2 5.9 + - - +
328A VAL* 3.0 33.6 + - + +
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Residues in contact with LEU 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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306A LEU* 3.3 20.7 - - + +
321A HIS* 5.2 2.2 - - + +
322A VAL* 3.1 29.1 + - + +
324A ALA* 1.3 79.6 - - + +
326A TYR* 1.3 57.1 + - - +
328A VAL* 3.4 8.0 + - + +
329A ALA* 2.8 36.7 + - - +
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Residues in contact with TYR 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156A TYR* 4.2 1.9 + - - -
227A HIS* 3.0 32.5 + + - -
228A ASP* 5.1 6.9 - - - -
306A LEU* 3.9 18.3 - - + +
307A LEU* 3.5 28.7 - - + -
310A HIS* 3.7 43.3 - + + +
311A TYR* 3.9 11.3 + - - -
322A VAL* 2.7 21.2 + - + +
323A TYR* 3.4 26.7 - + - +
325A LEU* 1.3 74.6 - - - +
327A ILE* 1.3 66.4 + - + +
329A ALA* 3.6 2.5 - - - +
330A LEU* 3.1 50.1 + - + +
2201A 8TZ 5.1 1.3 - + - -
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Residues in contact with ILE 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A VAL* 3.6 28.5 - - + -
69A LEU* 5.2 2.9 - - + -
73A LEU* 4.6 8.3 - - + -
74A THR* 3.7 15.3 - - + -
78A LEU* 3.7 21.5 - - + -
228A ASP* 5.5 4.5 - - + +
323A TYR* 3.1 31.4 + - + +
324A ALA* 3.6 9.0 - - - +
325A LEU 3.2 0.6 - - - -
326A TYR* 1.3 84.2 - - + +
328A VAL* 1.3 65.4 + - - +
330A LEU 3.3 0.3 + - - -
331A CYS* 3.0 19.4 + - - +
2201A 8TZ 3.1 39.5 - - + +
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Residues in contact with VAL 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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73A LEU* 4.0 29.4 - - + -
77A PHE* 4.9 12.8 - - + -
78A LEU* 5.2 1.3 - - - -
324A ALA 3.0 18.2 + - - +
325A LEU* 3.9 9.9 - - + +
327A ILE* 1.3 75.1 - - - +
329A ALA* 1.3 58.8 + - - +
331A CYS* 3.2 6.3 + - - +
332A LEU* 2.9 49.7 + - + +
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Residues in contact with ALA 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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298A ILE 4.9 1.4 - - - +
302A PRO* 3.6 37.2 - - + +
303A SER* 3.2 15.1 + - - -
306A LEU* 3.7 9.6 - - + -
325A LEU 2.8 18.8 + - - +
326A TYR* 3.6 6.5 - - - +
328A VAL* 1.3 77.8 - - - +
330A LEU* 1.3 62.1 + - + +
332A LEU* 3.4 5.9 + - - +
333A SER 3.0 18.9 + - - -
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Residues in contact with LEU 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 4.2 2.1 + - - -
155A PHE* 3.7 30.5 - - + -
156A TYR* 4.6 6.5 - - - +
159A MET* 5.1 1.1 - - + -
227A HIS* 3.5 20.0 - - + -
303A SER* 4.9 10.8 - - - -
307A LEU* 4.9 13.9 - - + -
326A TYR* 3.1 53.4 + - + +
327A ILE 3.3 0.2 + - - -
329A ALA* 1.3 79.5 - - + +
331A CYS* 1.3 60.9 + - - +
333A SER* 2.6 22.5 + - - +
334A THR* 3.5 9.9 - - - +
2201A 8TZ 3.6 27.8 - - + +
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Residues in contact with CYS 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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77A PHE* 4.2 10.3 - - + -
78A LEU* 3.5 30.1 - - + -
81A VAL* 3.6 34.7 - - - +
82A TYR* 3.5 22.2 + - - +
327A ILE 3.0 13.7 + - - +
328A VAL* 3.5 10.1 - - - +
330A LEU* 1.3 73.6 - - - +
332A LEU* 1.3 61.7 + - - +
333A SER 3.1 4.0 - - - -
334A THR* 2.8 27.7 + - - -
335A LEU* 4.2 0.5 + - - +
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A PHE* 5.1 13.7 - - + -
81A VAL* 5.4 4.5 - - + -
298A ILE* 4.0 25.7 - - + +
299A CYS* 3.4 8.8 - - - -
302A PRO* 6.1 3.4 - - + -
328A VAL* 2.9 37.5 + - + +
329A ALA* 4.0 5.8 - - - +
331A CYS* 1.3 79.1 - - + +
333A SER* 1.3 63.4 + - - +
334A THR 3.1 0.4 - - - -
335A LEU* 3.2 42.9 + - + +
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Residues in contact with SER 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A PHE* 3.6 17.5 - - - -
159A MET* 3.7 12.4 - - - +
299A CYS* 3.2 22.2 - - - +
300A PHE* 5.5 0.2 - - - -
303A SER* 3.1 25.8 - - - -
329A ALA 3.0 7.4 + - - -
330A LEU* 2.6 21.2 + - - -
332A LEU* 1.3 78.1 - - - +
334A THR* 1.3 51.1 + - - +
335A LEU 3.1 1.9 + - - -
336A ASN* 2.5 34.5 + - - -
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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
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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