Contacts of the helix formed by residues 312 - 323 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ASP* 5.7 1.8 - - - +
278A ARG 5.5 1.5 + - - -
311A ALA* 1.3 74.9 - - - +
313A ASN* 1.3 61.2 + - - +
314A ILE* 3.3 16.6 + - - +
315A SER* 3.3 22.5 + - - -
316A GLN* 2.9 26.7 + - - +
276B GLY 3.6 0.2 - - - -
277B VAL* 3.5 21.2 + - - +
278B ARG* 3.6 17.3 - - - +
312B SER* 5.1 8.0 + - - -
315B SER* 4.5 6.3 + - - -
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Residues in contact with ASN 313 (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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81A LYS* 3.6 22.6 + - - +
85A LEU* 3.5 30.9 - - - +
92A SER* 4.0 16.5 + - - +
93A GLY 4.4 2.7 + - - +
311A ALA 3.3 3.5 + - - +
312A SER* 1.3 68.8 - - - +
314A ILE* 1.3 73.6 + - - +
316A GLN* 3.8 12.2 - - - +
317A ALA* 3.2 16.1 + - - +
276B GLY* 3.0 35.4 + - - +
277B VAL* 3.8 12.7 - - - +
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Residues in contact with ILE 314 (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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78A MET* 3.4 33.1 - - + +
81A LYS* 3.9 13.5 - - + -
82A ALA* 4.0 18.2 - - + +
85A LEU* 3.9 17.5 - - + -
312A SER* 3.2 6.8 + - - +
313A ASN* 1.3 88.4 + - - +
315A SER* 1.3 66.2 + - - +
317A ALA* 3.3 3.8 + - - +
318A GLY 3.1 16.8 + - - -
78B MET* 3.8 33.4 - - + -
277B VAL* 4.4 5.8 - - + -
312B SER* 6.0 0.7 - - - +
314B ILE* 3.8 33.2 - - + -
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Residues in contact with SER 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A MET* 3.3 13.0 - - - +
274A PHE* 4.1 3.5 - - - -
277A VAL* 2.8 32.4 + - - +
278A ARG* 3.8 13.8 + - - +
279A LEU* 3.6 14.6 - - - +
312A SER* 3.3 23.8 + - - -
314A ILE* 1.3 79.4 - - - +
316A GLN* 1.3 57.0 + - - +
318A GLY* 3.2 2.6 + - - -
319A ALA* 3.0 24.1 + - - +
312B SER* 4.1 4.5 + - - -
314B ILE* 6.0 0.2 - - - +
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Residues in contact with GLN 316 (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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95A GLY 6.3 0.4 - - - -
96A ALA 4.8 4.2 + - - -
99A GLY* 3.6 9.8 - - - -
100A ALA* 2.7 43.4 + - + +
103A LEU* 3.8 22.5 - - + +
124A VAL* 4.2 4.7 - - + -
279A LEU* 3.5 19.7 - - + -
311A ALA* 2.8 33.8 + - + +
312A SER 2.9 16.0 + - - +
313A ASN* 4.0 10.7 - - - +
314A ILE 3.2 0.4 - - - -
315A SER* 1.3 73.6 - - - +
317A ALA* 1.4 56.6 + - - +
319A ALA* 3.4 1.1 + - - +
320A LEU* 2.9 34.8 + - - +
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Residues in contact with ALA 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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77A ALA* 3.7 19.7 - - + +
81A LYS* 3.7 28.3 - - + +
313A ASN 3.2 14.1 + - - +
314A ILE 3.3 9.2 + - - +
316A GLN* 1.4 74.3 - - - +
318A GLY* 1.3 64.3 + - - +
320A LEU* 3.5 11.1 - - - +
321A ALA 3.1 17.2 + - - -
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Residues in contact with GLY 318 (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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74A ILE* 3.5 29.4 - - - +
78A MET* 3.6 24.1 - - - +
274A PHE* 4.0 1.8 - - - -
314A ILE 3.1 11.3 + - - -
315A SER 3.2 5.6 + - - -
317A ALA* 1.3 76.4 - - - +
319A ALA* 1.3 59.6 + - - +
321A ALA* 3.3 5.5 + - - +
322A CYS* 3.2 15.2 + - - -
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Residues in contact with ALA 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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103A LEU* 4.1 8.1 - - + -
268A PHE* 3.3 33.7 - - + -
274A PHE* 4.0 5.2 - - + -
279A LEU* 3.9 13.7 - - + -
315A SER 3.0 15.9 + - - +
316A GLN 3.9 3.6 - - - +
318A GLY* 1.3 69.2 - - - +
320A LEU* 1.3 65.7 - - - +
322A CYS* 3.1 27.1 + - - +
323A LEU* 3.4 13.9 + - - +
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Residues in contact with LEU 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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102A PRO* 4.1 34.1 - - + +
103A LEU* 4.0 15.5 - - + +
106A ALA* 4.1 15.5 - - + -
316A GLN 2.9 18.6 + - - +
317A ALA* 3.5 11.9 - - - +
319A ALA* 1.3 76.6 - - - +
321A ALA* 1.3 59.6 + - - +
323A LEU* 3.2 14.2 + - - +
324A THR* 3.7 10.7 - - - +
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Residues in contact with ALA 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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73A VAL* 3.8 18.8 - - + +
74A ILE* 4.0 5.9 - - + +
77A ALA* 3.4 33.0 - - + -
317A ALA 3.1 3.6 + - - -
318A GLY 3.3 7.2 + - - +
320A LEU* 1.3 75.4 - - - +
322A CYS* 1.3 60.8 + - - +
323A LEU 3.2 0.2 - - - -
324A THR* 2.6 32.6 + - - -
327A GLY* 3.3 6.8 + - - -
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Residues in contact with CYS 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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74A ILE* 3.4 30.5 - - - -
268A PHE* 3.8 19.7 - - + -
272A ALA* 3.7 29.2 - - - -
274A PHE* 4.3 1.6 - - - -
318A GLY 3.2 14.6 + - - -
319A ALA* 3.1 19.1 + - - +
321A ALA* 1.3 81.1 - - - +
323A LEU* 1.3 56.1 + - - +
324A THR 3.1 0.6 + - - -
327A GLY* 3.3 2.1 - - - -
328A LEU* 3.1 32.2 + - - +
331A MET* 3.9 10.2 - - - +
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Residues in contact with LEU 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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103A LEU* 4.6 3.8 - - + -
106A ALA* 3.9 40.3 - - + +
107A ILE* 4.1 13.2 - - + -
110A THR* 4.0 20.4 + - + +
111A PHE* 3.6 31.9 - - + -
268A PHE* 3.7 21.1 - - + -
319A ALA 3.5 13.5 - - - +
320A LEU* 3.2 10.0 + - - +
321A ALA 3.2 1.0 - - - -
322A CYS* 1.3 81.5 - - + +
324A THR* 1.3 62.1 + - - +
328A LEU* 4.2 13.5 - - + -
331A MET* 5.4 0.9 - - + -
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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