Contacts of the helix formed by residues 307 - 324 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C THR* 6.0 0.7 - - - -
305C ASP* 2.5 23.0 + - - -
306C SER* 1.3 82.1 + - - +
308C LEU* 1.3 63.3 + - - +
309C ALA* 3.7 8.2 + - - +
310C THR* 3.1 18.7 + - - -
311C LYS* 3.1 22.1 + - - +
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Residues in contact with LEU 308 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306C SER 3.8 0.4 + - - -
307C SER* 1.3 73.5 - - - +
309C ALA* 1.3 56.6 + - - +
311C LYS* 3.4 15.6 + - + +
312C GLY* 2.8 27.9 + - - -
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Residues in contact with ALA 309 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307C SER* 3.2 8.4 - - - +
308C LEU* 1.3 79.1 - - - +
310C THR* 1.3 62.9 + - - +
312C GLY 3.2 3.8 + - - -
313C VAL* 3.3 4.5 + - - +
352C ASN* 6.2 2.0 - - - +
355C ASN* 2.7 46.0 + - - +
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Residues in contact with THR 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301C PRO* 3.6 26.4 - - + +
304C PRO* 4.7 3.4 - - + -
305C ASP* 2.4 60.0 + - - +
307C SER* 3.1 5.4 + - - -
309C ALA* 1.3 78.9 - - - +
311C LYS* 1.3 58.5 + - - +
313C VAL* 2.7 28.5 - - - +
314C VAL* 2.9 21.3 + - + +
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Residues in contact with LYS 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C THR* 4.5 24.5 + - - +
11C PRO 5.2 2.2 + - - -
12C THR* 5.2 4.2 - - - +
305C ASP 4.6 5.2 - - - +
306C SER* 3.2 39.7 + - - +
307C SER 3.1 16.1 + - - +
308C LEU* 3.7 17.2 - - + +
310C THR* 1.3 76.7 - - - +
312C GLY* 1.3 56.4 + - - +
314C VAL* 4.5 5.4 - - - +
315C HIS* 2.8 52.5 + - + +
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Residues in contact with GLY 312 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C CYS* 5.6 1.3 - - - -
308C LEU 2.8 17.8 + - - -
309C ALA 3.7 2.9 - - - -
310C THR 3.2 0.6 - - - -
311C LYS* 1.3 79.7 - - - +
313C VAL* 1.3 60.2 + - - +
315C HIS* 3.6 7.5 + - - +
316C ILE* 3.3 23.7 + - - +
355C ASN* 3.8 8.5 - - - -
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Residues in contact with VAL 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298C CYS* 3.7 29.8 - - + -
299C ILE 4.0 12.6 - - - +
300C LEU* 3.6 28.7 - - + -
301C PRO* 4.0 11.9 - - + -
309C ALA 3.3 9.2 + - - +
310C THR* 2.7 32.1 - - - +
312C GLY* 1.3 74.6 - - - +
314C VAL* 1.3 70.1 + - + +
315C HIS 3.1 0.2 - - - -
316C ILE* 3.1 9.9 + - - +
317C ASP* 3.1 18.7 + - - +
329C GLU* 3.8 13.6 - - + +
355C ASN* 3.6 5.9 + - - +
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Residues in contact with VAL 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C LEU* 4.1 13.0 - - + -
301C PRO* 5.4 0.9 - - + -
304C PRO* 6.2 2.7 - - + -
310C THR* 2.9 36.0 + - + +
311C LYS* 4.1 6.3 - - - +
313C VAL* 1.3 82.8 - - + +
315C HIS* 1.3 66.5 + - + +
317C ASP* 3.2 10.5 + - + +
318C VAL* 3.1 33.1 + - + +
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Residues in contact with HIS 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311C LYS* 2.8 44.8 + - + +
312C GLY* 3.6 7.6 - - - +
313C VAL 3.1 0.2 - - - -
314C VAL* 1.3 79.6 - - + +
316C ILE* 1.3 66.0 + - + +
318C VAL* 3.0 26.3 - - + +
319C ILE* 3.1 19.2 + - + +
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Residues in contact with ILE 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127C LEU* 6.4 1.3 - - + -
183C HIS* 5.6 10.5 - - + -
269C HIS* 4.4 14.4 - - + -
298C CYS* 5.4 8.5 - - - -
312C GLY 3.3 17.0 - - - +
313C VAL* 3.1 8.9 + - - +
315C HIS* 1.3 79.8 - - + +
317C ASP* 1.3 58.7 + - - +
319C ILE* 3.1 13.2 + - + +
320C MET* 2.8 37.2 + - - +
329C GLU* 3.9 22.2 - - - +
366C FER 3.8 25.1 - - + +
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Residues in contact with ASP 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300C LEU* 4.6 9.8 - - + +
313C VAL 3.1 8.5 + - - +
314C VAL* 3.5 14.6 - - + +
316C ILE* 1.3 77.1 - - - +
318C VAL* 1.3 64.0 + - + +
320C MET* 3.3 7.7 - - - +
321C LEU* 3.0 23.9 + - - +
328C LYS* 3.7 10.7 - - - +
329C GLU* 3.0 46.9 + - + +
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Residues in contact with VAL 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C TRP* 3.7 19.5 - - + -
314C VAL* 3.1 24.0 + - + +
315C HIS* 3.0 24.5 - - + +
317C ASP* 1.3 79.5 - - - +
319C ILE* 1.3 67.7 + - + +
320C MET 3.1 1.6 - - - -
321C LEU* 3.0 20.8 + - + +
322C ALA* 2.9 21.8 + - - +
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Residues in contact with ILE 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ASN* 3.5 30.3 - - + +
140C TRP* 4.3 18.8 - - + -
315C HIS* 3.1 27.0 + - + +
316C ILE* 3.1 18.3 + - + +
318C VAL* 1.3 78.5 - - + +
320C MET* 1.3 64.5 + - + +
322C ALA* 3.1 2.8 + - - +
323C HIS* 3.0 42.9 + - + +
366C FER 4.0 32.3 - - + +
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Residues in contact with MET 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269C HIS* 3.9 20.2 - - - +
270C ASP* 4.8 6.5 - - - +
316C ILE* 2.8 20.3 + - - +
317C ASP* 3.3 13.9 - - - +
319C ILE* 1.3 81.3 - - + +
321C LEU* 1.3 57.7 + - - +
323C HIS* 4.8 1.1 - - + -
324C ASN* 2.4 82.3 + - + +
327C GLY* 3.5 19.1 - - - +
328C LYS* 3.8 4.3 - - - +
329C GLU* 4.8 5.8 - - - +
366C FER 3.4 43.7 - - + -
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Residues in contact with LEU 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140C TRP* 6.1 0.4 - - + -
143C LEU* 4.2 31.9 - - + -
152C ILE* 4.5 2.9 - - - +
153C PRO* 3.4 17.2 - - + +
317C ASP* 3.0 14.9 + - - +
318C VAL* 3.0 24.7 + - + +
320C MET* 1.3 76.8 - - - +
322C ALA* 1.3 58.6 + - + +
324C ASN* 3.4 6.2 - - - +
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Residues in contact with ALA 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C SER* 3.9 7.6 - - - -
140C TRP* 3.8 26.9 - - + -
143C LEU* 5.7 1.1 - - + -
152C ILE* 3.8 0.6 - - - +
153C PRO* 3.3 15.9 - - + +
154C PHE 3.0 26.5 + - - -
318C VAL 2.9 11.7 + - - +
319C ILE 3.1 8.5 + - - +
321C LEU* 1.3 80.0 - - - +
323C HIS* 1.3 76.6 + - + +
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Residues in contact with HIS 323 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131C ASN* 5.7 0.6 + - - -
136C LEU* 3.2 56.1 + - + +
139C SER* 2.8 35.7 + - - -
140C TRP* 5.0 8.4 + - - -
152C ILE* 4.1 5.5 - - - +
154C PHE* 3.8 18.3 - - + +
155C ASN* 4.9 2.3 + - - -
162C ALA* 4.1 18.2 + - + +
319C ILE* 3.0 35.2 + - + +
320C MET* 4.8 2.0 - - + -
322C ALA* 1.3 85.7 - - + +
324C ASN* 1.3 65.5 + - - +
325C PRO* 4.1 1.4 - - - +
366C FER 4.9 19.0 + + + +
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Residues in contact with ASN 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ILE* 3.2 22.5 - - - +
270C ASP* 4.9 1.6 - - - +
320C MET* 2.4 73.4 + - + +
321C LEU* 3.4 6.5 - - - +
323C HIS* 1.3 72.8 - - - +
325C PRO* 1.3 72.5 - - + +
326C GLY* 2.6 7.6 + - - -
327C GLY* 2.4 49.0 + - - +
366C FER 5.8 1.8 - - - -
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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
------------------------------------------------------------
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