Contacts of the helix formed by residues 312 - 323 (chain B) in PDB entry 2Z1Z
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 SER 312 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A GLY 3.5 6.5 - - - -
277A VAL* 3.5 22.9 + - - +
278A ARG* 3.9 7.9 - - - +
312A SER* 5.1 7.7 + - - -
314A ILE* 6.0 0.3 - - - +
315A SER* 4.1 8.0 + - - -
126B ASP* 5.5 1.2 - - - +
278B ARG 5.3 1.0 + - - -
310B GLY 3.6 1.0 + - - -
311B ALA* 1.3 72.9 - - - +
313B ASN* 1.3 62.9 + - - +
314B ILE* 3.4 16.1 + - - +
315B SER* 3.2 21.6 + - - -
316B GLN* 2.9 31.6 + - - +
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Residues in contact with ASN 313 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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276A GLY* 2.9 45.7 + - - +
277A VAL* 3.5 17.3 - - - +
81B LYS* 3.9 20.1 + - - +
85B LEU* 3.5 27.9 - - - +
91B TYR* 5.6 0.8 - - - -
92B SER* 3.8 15.3 - - - -
93B GLY 4.5 2.1 - - - +
311B ALA 3.7 2.2 + - - -
312B SER* 1.3 71.1 + - - +
314B ILE* 1.3 68.8 + - - +
316B GLN* 3.5 10.2 + - - +
317B ALA* 3.0 28.2 + - - +
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Residues in contact with ILE 314 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A MET* 4.0 24.0 - - + -
82A ALA* 5.5 0.2 - - + -
277A VAL* 4.7 2.7 - - + -
314A ILE* 3.8 40.4 - - + -
78B MET* 3.2 31.6 - - + +
81B LYS* 3.8 21.5 - - + -
82B ALA* 3.9 24.5 - - + +
85B LEU* 3.9 17.3 - - + -
312B SER* 3.2 7.9 + - - +
313B ASN* 1.3 80.4 + - - +
315B SER* 1.3 61.2 + - - +
317B ALA* 3.4 3.3 + - - +
318B GLY 3.0 21.3 + - - -
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Residues in contact with SER 315 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A SER* 4.5 2.8 + - - -
314A ILE* 5.8 0.2 - - - +
78B MET* 3.4 9.1 - - - +
274B PHE* 3.7 4.2 - - - -
277B VAL* 3.1 30.6 + - - +
278B ARG 3.6 18.9 + - - -
279B LEU* 3.5 15.2 - - - +
312B SER* 3.2 23.2 + - - -
314B ILE* 1.3 75.7 - - - +
316B GLN* 1.3 54.1 + - - +
318B GLY* 3.1 3.3 + - - -
319B ALA* 2.7 30.0 + - - +
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Residues in contact with GLN 316 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B ALA 5.0 4.2 + - - -
99B GLY* 3.8 14.2 - - - -
100B ALA* 2.8 39.6 + - + +
103B LEU* 3.7 22.7 - - + +
124B VAL* 4.3 1.1 - - + -
279B LEU* 3.6 14.8 - - + -
310B GLY* 4.9 0.8 - - - -
311B ALA* 3.2 33.7 + - + +
312B SER 2.9 17.6 + - - +
313B ASN* 3.7 9.0 - - - +
315B SER* 1.3 73.6 - - - +
317B ALA* 1.3 57.3 + - - +
319B ALA* 3.1 2.4 + - - +
320B LEU* 2.9 31.3 + - - +
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Residues in contact with ALA 317 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ALA* 3.8 13.0 - - + +
78B MET* 4.8 0.2 - - - -
81B LYS* 3.6 31.4 - - + +
313B ASN 3.0 17.6 + - - +
314B ILE 3.5 6.7 - - - +
316B GLN* 1.3 72.8 - - - +
318B GLY* 1.3 64.6 + - - +
320B LEU* 3.6 7.1 + - - +
321B ALA* 3.2 21.3 + - - +
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Residues in contact with GLY 318 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ILE* 3.8 9.8 - - - +
78B MET* 3.6 22.1 - - - +
274B PHE* 3.9 12.6 - - - -
314B ILE 3.0 10.7 + - - -
315B SER 3.1 4.9 + - - -
317B ALA* 1.3 76.6 - - - +
319B ALA* 1.3 60.9 + - - +
321B ALA* 3.0 13.6 + - - +
322B CYS* 3.1 16.3 + - - -
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Residues in contact with ALA 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 3.9 11.9 - - + -
268B PHE* 3.5 32.9 - - + -
274B PHE* 4.0 4.0 - - + -
279B LEU* 3.6 15.9 - - + -
315B SER 2.7 18.3 + - - +
316B GLN 3.1 4.9 + - - +
318B GLY* 1.3 71.8 - - - +
320B LEU* 1.3 62.6 + - - +
322B CYS* 3.0 19.4 + - - +
323B LEU* 3.4 15.1 + - - +
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Residues in contact with LEU 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B PRO* 3.5 38.1 - - + +
103B LEU* 3.8 18.7 - - + +
106B ALA* 4.1 11.7 - - + -
316B GLN 2.9 16.1 + - - +
317B ALA* 3.7 9.2 - - - +
319B ALA* 1.3 76.3 - - - +
321B ALA* 1.3 61.1 + - - +
323B LEU* 3.3 15.0 + - - +
324B THR* 3.5 12.0 - - - +
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Residues in contact with ALA 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B VAL* 4.2 15.5 - - + +
74B ILE* 4.0 7.3 - - + +
77B ALA* 3.4 33.9 - - + -
317B ALA 3.2 4.6 + - - +
318B GLY 3.0 9.6 + - - +
320B LEU* 1.3 76.3 - - - +
322B CYS* 1.3 57.7 + - - +
324B THR* 2.8 28.9 + - - -
326B GLU* 4.8 1.1 - - - +
327B GLY* 3.3 6.8 + - - -
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Residues in contact with CYS 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ILE* 2.9 35.4 - - + -
268B PHE* 4.0 11.9 - - + -
272B ALA* 3.9 22.2 - - - -
274B PHE* 4.4 2.7 - - - -
318B GLY 3.1 16.2 + - - -
319B ALA* 3.0 15.2 + - - +
321B ALA* 1.3 78.6 - - - +
323B LEU* 1.3 57.9 + - - +
324B THR 2.9 8.2 + - - +
327B GLY* 3.2 3.7 - - - -
328B LEU* 3.1 25.6 + - - +
331B MET* 3.7 19.7 - - - -
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B LEU* 4.4 4.0 - - + -
106B ALA* 3.7 21.8 - - + +
107B ILE* 3.7 43.3 - - + +
110B THR* 4.0 20.4 + - + +
111B PHE* 3.7 29.8 - - + -
268B PHE* 4.0 17.0 - - + -
319B ALA 3.6 10.8 - - - +
320B LEU* 3.3 9.8 + - - +
322B CYS* 1.3 81.7 - - + +
324B THR* 1.3 64.8 + - - +
328B LEU* 4.1 13.9 - - + -
331B MET* 4.6 0.4 - - + -
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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