Contacts of the helix formed by residues 307 - 324 (chain E) in PDB entry 1KYZ
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 307 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5E GLY 4.1 9.0 - - - +
8E GLN* 4.0 3.6 - - - +
305E ASP* 2.5 23.0 + - - -
306E SER* 1.3 81.8 + - - +
308E LEU* 1.3 59.1 - - - +
309E ALA* 3.7 8.1 + - - +
310E THR* 3.2 17.3 + - - -
311E LYS* 3.0 28.1 + - - +
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Residues in contact with LEU 308 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A GLU* 4.1 10.5 - - + +
21A LEU* 3.7 26.6 - - + +
22A PHE* 3.8 22.2 - - + +
25A GLN* 3.5 41.9 - - + +
5E GLY* 3.2 33.4 - - - +
7E THR 3.3 17.9 - - - +
8E GLN* 3.5 21.4 - - + +
307E SER* 1.3 70.6 - - - +
309E ALA* 1.3 56.4 + - - +
311E LYS* 3.8 4.5 - - + +
312E GLY* 2.8 31.5 + - - -
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Residues in contact with ALA 309 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 3.8 17.4 - - + +
5E GLY 4.8 1.0 - - - +
307E SER* 3.2 8.4 + - - +
308E LEU* 1.3 79.4 - - - +
310E THR* 1.3 61.8 + - - +
312E GLY 3.3 3.6 + - - -
313E VAL* 3.3 6.1 + - - +
355E ASN* 3.0 41.9 + - - +
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Residues in contact with THR 310 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A CYS* 4.0 13.9 - - - -
301E PRO* 3.5 28.0 - - + +
303E ALA 4.7 0.7 - - - +
304E PRO* 4.7 0.9 - - + -
305E ASP* 2.4 54.9 + - - +
307E SER* 3.2 6.0 + - - -
309E ALA* 1.3 75.2 - - - +
311E LYS* 1.3 67.1 + - - +
313E VAL* 2.9 25.0 - - - +
314E VAL* 2.9 13.6 + - + +
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Residues in contact with LYS 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLN* 3.8 14.5 - - + +
86A CYS* 3.4 38.0 + - + -
87A TYR* 3.7 48.1 - - + +
8E GLN* 2.6 28.9 + - - +
10E THR* 4.5 4.4 + - - -
11E PRO 5.6 0.2 + - - -
12E THR* 4.6 4.2 - - - +
305E ASP 4.5 0.7 - - - +
306E SER* 3.1 19.6 + - - +
307E SER 3.0 20.2 + - - +
308E LEU* 3.8 6.1 - - + +
310E THR* 1.3 75.4 - - - +
312E GLY* 1.3 64.6 + - - +
314E VAL* 4.4 6.1 - - - +
315E HIS* 2.8 35.1 + - + +
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Residues in contact with GLY 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LEU* 5.6 1.6 - - - -
24A MET* 5.5 14.6 - - - +
25A GLN* 6.0 3.1 - - - +
298E CYS* 5.2 1.1 - - - -
308E LEU 2.8 18.4 + - - -
309E ALA 3.3 3.6 + - - -
310E THR 3.1 0.6 - - - -
311E LYS* 1.3 79.3 - - - +
313E VAL* 1.3 59.8 + - - +
315E HIS* 3.6 6.7 - - - +
316E ILE* 3.3 24.8 + - - +
355E ASN* 3.9 10.8 - - - -
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Residues in contact with VAL 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298E CYS* 3.6 31.9 - - + -
299E ILE 4.1 4.9 - - - +
300E LEU* 3.6 31.4 - - + +
301E PRO* 4.1 11.9 - - + -
309E ALA 3.3 9.1 + - - +
310E THR* 2.9 30.5 - - - +
312E GLY* 1.3 75.4 - - - +
314E VAL* 1.3 65.3 + - + +
316E ILE* 3.3 2.8 + - - +
317E ASP* 3.1 17.3 + - - +
329E GLU* 3.4 27.6 - - + +
355E ASN* 3.8 1.9 - - - +
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Residues in contact with VAL 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ARG 4.8 0.4 - - - +
82A ARG* 4.2 17.9 - - + +
83A LEU* 3.6 44.6 - - + +
86A CYS* 3.7 22.2 - - - -
300E LEU* 4.1 16.8 - - + -
301E PRO* 5.6 0.4 - - + -
304E PRO* 6.1 0.2 - - + -
310E THR* 2.9 27.1 + - + +
311E LYS* 4.0 3.6 - - - +
313E VAL* 1.3 76.2 - - - +
315E HIS* 1.3 63.3 + - - +
317E ASP* 3.1 8.2 + - + +
318E VAL* 3.0 25.4 + - + +
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Residues in contact with HIS 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A MET 4.5 0.6 + - - -
25A GLN* 3.7 26.2 + - + +
28A SER* 2.7 43.8 + - - +
29A ALA* 4.4 4.5 - - - -
31A VAL* 4.2 11.1 - - + +
32A LEU* 5.4 1.9 + - + -
83A LEU* 3.7 22.4 - - + +
87A TYR* 2.6 34.4 + + - -
311E LYS* 2.8 30.7 + - - +
312E GLY* 3.6 8.5 - - - +
313E VAL 3.2 0.2 - - - -
314E VAL* 1.3 77.5 - - - +
316E ILE* 1.3 63.7 + - + +
318E VAL* 3.4 2.9 + - - +
319E ILE* 3.0 29.3 + - - +
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Residues in contact with ILE 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A MET* 5.1 15.0 - - + -
28A SER* 5.0 4.5 - - - +
131E ASN* 6.0 0.4 - - - +
269E HIS* 4.0 14.8 - - + -
298E CYS* 5.1 9.2 - - - -
312E GLY 3.3 17.0 - - - +
313E VAL* 3.3 6.9 + - - +
314E VAL 3.3 0.4 - - - -
315E HIS* 1.3 77.9 - - + +
317E ASP* 1.3 60.7 + - - +
319E ILE* 3.1 15.2 + - + +
320E MET* 2.8 33.5 + - - +
329E GLU* 3.5 22.7 - - - +
1698E FER 3.6 30.1 - - - +
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Residues in contact with ASP 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ARG* 2.8 65.4 + - - +
82A ARG* 3.1 27.2 + - - +
300E LEU* 5.0 1.6 - - + -
313E VAL 3.1 12.7 + - - +
314E VAL* 3.1 14.2 + - + +
316E ILE* 1.3 77.8 - - - +
318E VAL* 1.3 56.1 + - - +
320E MET* 3.3 4.4 - - - +
321E LEU 3.0 10.0 + - - -
328E LYS* 3.5 3.3 - - - +
329E GLU* 3.0 39.0 + - + +
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Residues in contact with VAL 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A VAL* 3.8 8.7 - - + -
35A ILE* 3.3 38.8 - - + -
79A ARG* 3.5 28.9 - - + +
80A MET* 4.6 0.2 - - - -
83A LEU* 4.1 17.9 - - + -
140E TRP* 3.6 12.5 - - + -
314E VAL* 3.0 19.8 + - + +
315E HIS 3.8 3.8 - - - +
317E ASP* 1.3 75.8 - - - +
319E ILE* 1.3 67.0 + - - +
320E MET 3.1 1.8 - - - -
321E LEU* 3.1 11.5 + - + +
322E ALA* 3.0 21.5 + - - +
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Residues in contact with ILE 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A SER* 3.7 30.1 - - - +
31A VAL* 3.7 14.1 - - + -
131E ASN* 3.7 17.7 - - + +
140E TRP* 4.3 11.7 - - + -
315E HIS 3.0 23.2 + - - +
316E ILE* 3.5 20.0 - - + +
318E VAL* 1.3 76.1 - - - +
320E MET* 1.3 62.8 + - + +
322E ALA* 3.2 1.8 + - - +
323E HIS* 3.1 50.7 + - + +
1698E FER 4.0 28.9 - - + +
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Residues in contact with MET 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ARG* 3.7 7.0 - - - +
269E HIS* 3.7 20.2 - - - +
270E ASP* 3.5 16.6 - - - +
316E ILE* 2.8 15.2 + - + +
317E ASP* 3.3 13.0 - - - +
318E VAL 3.1 0.2 - - - -
319E ILE* 1.3 78.8 - - - +
321E LEU* 1.3 60.6 + - - +
323E HIS* 4.9 0.7 - - + -
324E ASN* 2.8 61.2 + - + +
327E GLY* 3.1 33.7 - - - +
328E LYS* 3.5 3.8 - - - +
329E GLU* 5.4 0.9 - - - +
1698E FER 3.2 38.1 - - + -
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Residues in contact with LEU 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A MET* 3.6 56.8 - - + +
79A ARG* 3.5 37.4 - - + +
80A MET* 3.9 17.3 - - + +
143E LEU* 4.4 18.4 - - + -
152E ILE* 4.6 1.6 - - - +
153E PRO* 3.6 13.7 - - - +
317E ASP 3.0 12.3 + - - +
318E VAL* 3.1 15.9 + - + +
320E MET* 1.3 77.3 - - - +
322E ALA* 1.3 61.0 + - + +
324E ASN 4.3 6.8 - - - +
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Residues in contact with ALA 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E SER* 3.7 5.6 + - - -
140E TRP* 3.6 37.5 - - + -
143E LEU* 5.6 1.8 - - + -
153E PRO* 3.2 18.6 - - + +
154E PHE* 3.1 25.3 + - - +
318E VAL 3.0 6.1 + - - +
319E ILE 3.5 8.3 - - - +
320E MET 3.1 0.4 - - - -
321E LEU* 1.3 80.0 - - + +
323E HIS* 1.3 73.6 + - + +
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Residues in contact with HIS 323 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E ASN* 5.8 0.9 - - - -
136E LEU* 3.1 55.0 + - + +
139E SER* 2.9 31.6 + - - -
140E TRP* 5.0 7.8 - + - -
152E ILE* 4.0 8.0 - - - +
154E PHE* 3.8 19.5 - + + +
155E ASN* 4.5 2.8 + - - -
162E ALA* 3.9 18.0 + - + +
319E ILE* 3.1 41.4 + - + +
320E MET* 4.9 1.3 - - + -
322E ALA* 1.3 84.1 - - + +
324E ASN* 1.3 59.6 + - - +
325E PRO* 4.2 3.6 - - - +
1698E FER 4.5 21.6 - - + +
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Residues in contact with ASN 324 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79A ARG* 5.7 0.7 + - - -
152E ILE* 4.4 5.6 - - - +
270E ASP* 2.8 48.1 + - - +
320E MET* 2.8 47.2 + - + +
321E LEU* 4.3 7.4 - - - +
323E HIS* 1.3 73.6 - - - +
325E PRO* 1.3 90.8 - - - +
326E GLY* 2.8 13.2 + - - -
327E GLY 3.0 12.5 + - - +
1698E FER 4.1 8.1 + - + -
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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
------------------------------------------------------------
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