Contacts of the helix formed by residues 307 - 324 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASP* 2.6 29.4 + - - -
306A SER* 1.3 75.2 - - - +
308A LEU* 1.3 59.7 + - - +
309A ALA* 3.8 7.4 + - - +
310A THR* 2.8 19.9 + - - -
311A LYS* 2.9 27.9 + - - +
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Residues in contact with LEU 308 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306A SER 3.8 1.5 + - - +
307A SER* 1.3 73.2 - - - +
309A ALA* 1.3 57.9 + - - +
311A LYS* 3.8 9.2 - - + +
312A GLY* 2.8 27.0 + - - -
11E PRO* 4.3 14.6 - - + -
14E ILE* 3.7 29.2 - - + -
18E GLU* 4.1 16.4 - - + +
21E LEU* 3.7 28.7 - - + +
22E PHE* 4.1 13.2 - - - +
25E GLN* 3.5 45.1 - - + +
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Residues in contact with ALA 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A SER* 3.2 7.7 + - - +
308A LEU* 1.3 77.8 - - - +
310A THR* 1.3 64.6 + - - +
312A GLY 3.3 0.2 + - - -
313A VAL* 3.3 12.0 + - - +
355A ASN* 2.9 40.7 + - - +
21E LEU* 4.1 19.9 - - + +
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Residues in contact with THR 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PRO* 3.9 24.6 - - + +
304A PRO* 4.7 2.7 - - + -
305A ASP* 2.6 60.4 + - - +
307A SER* 2.8 10.5 + - - -
309A ALA* 1.3 76.8 - - - +
311A LYS* 1.3 66.8 + - - +
313A VAL* 3.0 8.7 + - - +
314A VAL* 3.0 26.4 + - + +
86E CYS* 4.0 11.0 - - - -
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Residues in contact with LYS 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305A ASP 4.5 0.2 - - - +
306A SER* 3.2 29.1 + - - +
307A SER 2.9 16.5 + - - +
308A LEU* 3.8 9.9 - - + +
310A THR* 1.3 76.2 - - - +
312A GLY* 1.3 56.9 + - - +
314A VAL* 4.5 5.8 - - - -
315A HIS* 2.8 41.3 + - + +
8E GLN 5.2 3.4 + - - -
9E ILE 4.3 7.1 + - - -
10E THR* 5.8 0.6 - - - +
11E PRO* 6.2 0.8 - - - +
25E GLN* 3.7 13.9 - - + +
83E LEU* 5.9 0.2 - - - -
86E CYS* 3.2 37.8 + - + -
87E TYR* 3.5 53.1 - - + +
88E ILE* 6.1 0.2 - - - +
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Residues in contact with GLY 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308A LEU 2.8 17.9 + - - -
309A ALA 3.7 2.9 - - - -
310A THR 3.1 0.6 - - - -
311A LYS* 1.3 78.5 - - - +
313A VAL* 1.3 60.1 + - - +
315A HIS* 3.6 7.1 - - - +
316A ILE* 3.5 28.5 + - - +
355A ASN* 3.9 9.2 - - - -
21E LEU* 6.0 0.9 - - - -
24E MET* 5.7 10.3 - - - -
25E GLN* 5.9 5.6 - - - +
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Residues in contact with VAL 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298A CYS* 3.7 32.1 - - + -
299A ILE 3.8 21.8 - - - +
300A LEU* 3.4 31.0 - - + -
301A PRO* 5.5 0.9 - - + -
309A ALA 3.3 15.7 - - - +
310A THR* 3.0 9.5 + - - +
312A GLY* 1.3 74.0 - - - +
314A VAL* 1.3 60.9 + - - +
316A ILE* 3.1 6.7 + - - +
317A ASP 3.0 21.5 + - - -
329A GLU* 3.6 11.2 - - + +
355A ASN* 3.5 14.1 - - - +
357A TYR* 6.4 0.7 - - + -
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LEU* 3.8 18.6 - - + -
310A THR* 3.0 20.7 + - + +
311A LYS* 4.0 3.1 - - - +
313A VAL* 1.3 72.3 - - - +
315A HIS* 1.3 66.3 + - - +
317A ASP* 3.1 9.8 + - + +
318A VAL* 3.0 25.7 + - + +
79E ARG 4.7 1.1 - - - +
82E ARG* 4.1 18.4 - - + +
83E LEU* 3.7 43.3 - - + +
86E CYS* 3.9 22.0 - - - -
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Residues in contact with HIS 315 (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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311A LYS* 2.8 31.0 + - - +
312A GLY* 3.6 9.4 - - - +
313A VAL 3.2 0.2 - - - -
314A VAL* 1.3 77.9 - - - +
316A ILE* 1.3 58.2 + - + +
318A VAL* 3.3 2.9 + - - +
319A ILE* 3.0 33.3 + - - +
24E MET 4.6 0.2 + - - -
25E GLN* 3.4 32.7 + - + +
28E SER* 2.6 40.8 + - - +
29E ALA* 4.1 5.4 - - - -
31E VAL* 4.2 9.8 - - + +
32E LEU* 5.5 2.1 + - + +
83E LEU* 3.9 19.5 - - + +
87E TYR* 2.6 33.7 + + - -
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Residues in contact with ILE 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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183A HIS* 5.3 12.6 - - + -
269A HIS* 4.4 10.8 - - + +
298A CYS* 3.9 25.6 - - - -
312A GLY 3.5 16.8 - - - +
313A VAL 3.1 7.0 + - - +
315A HIS* 1.3 76.3 - - + +
317A ASP* 1.3 66.4 + - - +
319A ILE* 3.7 10.4 - - + +
320A MET* 2.9 27.0 + - + +
329A GLU* 3.5 20.4 - - - +
366A FER 4.2 26.7 - - - +
24E MET* 5.3 9.6 - - + -
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Residues in contact with ASP 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LEU* 5.1 1.3 - - + -
313A VAL 3.0 9.3 + - - +
314A VAL* 3.1 14.1 + - + +
316A ILE* 1.3 76.0 - - - +
318A VAL* 1.3 63.1 + - - +
320A MET* 3.4 3.6 - - - +
321A LEU* 3.2 4.7 + - - +
328A LYS* 3.6 2.8 - - - +
329A GLU* 2.9 46.0 + - + +
79E ARG* 2.8 65.1 + - - +
82E ARG* 3.2 25.8 + - - +
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Residues in contact with VAL 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A TRP* 3.5 11.0 - - + -
314A VAL* 3.0 19.5 + - + +
315A HIS 3.7 3.8 - - - +
317A ASP* 1.3 76.4 - - - +
319A ILE* 1.3 63.9 + - - +
321A LEU* 3.1 24.4 - - + +
322A ALA 3.2 4.5 + - - -
31E VAL* 3.3 16.2 - - + -
35E ILE* 3.2 40.6 - - + -
79E ARG 3.7 25.8 - - - +
80E MET* 4.8 0.4 - - - -
83E LEU* 4.1 19.1 - - + -
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Residues in contact with ILE 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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131A ASN* 3.9 12.6 - - + +
136A LEU* 6.4 0.2 - - + -
140A TRP* 4.3 11.4 - - + -
315A HIS 3.0 21.7 + - - +
316A ILE* 3.7 11.7 - - + +
318A VAL* 1.3 75.4 - - - +
320A MET* 1.3 64.8 + - + +
322A ALA* 3.0 11.1 + - - +
323A HIS* 3.2 34.6 - - + +
366A FER 3.8 38.8 - - + +
28E SER* 3.8 28.3 - - - +
31E VAL* 3.7 14.1 - - + -
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Residues in contact with MET 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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269A HIS* 3.4 34.8 - - - +
270A ASP* 3.6 16.6 - - - +
316A ILE* 2.9 16.6 + - + +
317A ASP* 3.4 13.5 - - - +
319A ILE* 1.3 80.3 - - + +
321A LEU* 1.3 57.1 + - - +
323A HIS* 5.4 1.3 - - + -
324A ASN* 2.7 58.0 + - + +
327A GLY* 3.2 32.5 - - - +
328A LYS* 3.6 2.9 - - - +
329A GLU* 4.9 1.6 - - - +
366A FER 4.6 27.8 - - + -
79E ARG* 3.7 4.3 - - - +
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Residues in contact with LEU 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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143A LEU* 4.0 21.3 - - + -
152A ILE* 4.8 0.5 - - - +
153A PRO* 3.6 12.1 - - + +
317A ASP 3.2 9.8 + - - +
318A VAL* 3.1 17.2 + - - +
320A MET* 1.3 80.9 - - - +
322A ALA* 1.3 58.9 + - - +
323A HIS 3.7 0.2 + - - -
324A ASN 4.2 7.3 + - - +
35E ILE* 4.8 3.6 - - + -
76E MET* 4.0 41.1 - - + +
79E ARG* 3.5 31.8 - - + +
80E MET* 3.8 30.7 - - + +
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Residues in contact with ALA 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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139A SER* 3.8 9.4 - - - -
140A TRP* 3.8 31.2 - - + -
143A LEU* 5.5 1.6 - - + -
152A ILE* 3.7 0.2 - - - +
153A PRO* 3.1 19.8 - - + +
154A PHE* 3.0 26.0 + - - +
318A VAL 3.2 0.8 + - - -
319A ILE 3.0 10.5 + - - +
321A LEU* 1.3 81.9 - - - +
323A HIS* 1.3 76.2 + - + +
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Residues in contact with HIS 323 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A LEU* 3.2 41.2 - - + +
139A SER* 2.8 34.6 + - - -
140A TRP* 5.0 6.7 + + - -
152A ILE* 2.9 18.1 - - - +
154A PHE* 3.8 13.5 - - + +
155A ASN* 4.7 0.9 + - - -
162A ALA* 4.3 14.2 - - - +
319A ILE* 3.2 43.2 + - + +
320A MET* 5.5 1.3 - - + -
322A ALA* 1.3 83.2 - - + +
324A ASN* 1.3 59.6 + - + +
325A PRO* 4.0 2.6 - - - +
366A FER 3.9 35.1 + + + +
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Residues in contact with ASN 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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152A ILE* 3.3 7.2 - - - +
270A ASP* 2.4 45.6 + - - +
320A MET* 2.7 48.8 + - + +
321A LEU* 4.2 6.2 - - - +
323A HIS* 1.3 74.3 - - - +
325A PRO* 1.3 100.4 - - - +
326A GLY 3.6 2.8 + - - -
327A GLY* 3.2 12.0 + - - +
366A FER 4.7 7.9 - - + +
79E ARG* 5.9 0.3 + - - -
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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