Contacts of the helix formed by residues 309 - 321 (chain C) in PDB entry 5UH6
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 ALA 309 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C PRO* 5.1 0.4 - - + -
207C SER* 3.5 25.5 - - - +
307C ASP* 4.7 5.8 - - - +
308C LEU* 1.3 75.1 - - - +
310C ARG* 1.3 59.3 + - - +
311C VAL* 3.1 22.4 - - + -
312C GLY* 2.8 4.8 + - - +
313C ARG* 2.7 30.8 + - - +
331C SER* 5.7 2.0 - - - -
377C ARG* 6.0 0.7 - - - +
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Residues in contact with ARG 310 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C VAL* 5.0 15.1 - - - +
88C GLU* 2.9 49.8 + - - +
92C GLU* 4.7 2.8 + - - +
309C ALA* 1.3 75.0 - - - +
311C VAL* 1.3 57.6 + - - +
313C ARG* 4.2 2.1 - - - +
314C TYR* 3.1 30.0 + - - +
328C ILE* 4.0 33.7 + - + +
330C SER 5.9 0.2 - - - -
331C SER* 6.0 2.2 - - - +
509C PHE* 3.5 19.7 - - + -
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Residues in contact with VAL 311 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C SER* 3.4 24.2 - - - +
183C PRO* 4.1 11.7 - - + -
309C ALA* 3.7 17.5 - - + -
310C ARG* 1.3 76.9 - - - +
312C GLY* 1.3 57.9 + - - +
314C TYR* 4.3 1.8 - - + -
315C LYS* 2.7 40.9 + - + +
377C ARG* 3.6 43.1 - - - +
509C PHE* 4.0 18.0 - - + +
511C PHE* 3.8 17.5 - - + -
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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
----------------------------------------------------------
183C PRO* 3.7 25.6 - - - -
184C GLY* 4.4 0.3 - - - -
308C LEU* 3.6 17.6 - - - +
309C ALA 2.8 11.3 + - - +
311C VAL* 1.3 83.7 - - - +
313C ARG* 1.3 59.3 + - - -
315C LYS* 4.3 0.7 - - - +
316C VAL* 3.1 31.0 + - - +
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Residues in contact with ARG 313 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308C LEU* 3.7 16.4 - - + +
309C ALA 2.7 17.0 + - - +
310C ARG 4.2 3.1 - - - +
312C GLY* 1.3 71.9 - - - +
314C TYR* 1.3 59.9 + - - +
316C VAL* 3.3 26.2 + - - +
317C ASN* 2.8 61.3 + - - +
322C LEU* 5.9 0.4 - - - -
328C ILE* 4.7 12.3 - - + -
330C SER* 3.3 45.1 + - - +
331C SER* 5.1 0.2 - - - -
332C THR 2.6 33.9 + - - +
333C LEU* 3.9 0.6 - - - +
334C THR* 4.1 4.4 - - - +
337C ASP* 2.7 40.3 + - - +
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Residues in contact with TYR 314 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310C ARG 3.1 19.3 + - - +
311C VAL* 3.9 3.4 - - - +
313C ARG* 1.3 79.3 - - - +
315C LYS* 1.3 65.4 + - + +
317C ASN* 3.5 8.2 + - + +
318C LYS* 3.2 65.2 + - + +
328C ILE* 5.0 12.8 - - + +
509C PHE* 3.7 36.6 - + + -
511C PHE* 4.9 13.0 - + - -
535C GLU* 5.0 6.9 + - - -
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Residues in contact with LYS 315 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182C SER* 4.0 10.3 - - - +
183C PRO 3.6 22.0 - - - +
184C GLY* 4.6 4.0 - - - -
185C VAL* 5.0 1.4 + - - +
186C TYR* 4.3 8.7 - - + +
311C VAL* 2.7 23.8 + - + +
312C GLY 4.3 0.2 - - - +
314C TYR* 1.3 74.1 - - + +
316C VAL* 1.3 64.5 + - - +
318C LYS* 3.4 22.7 + - - +
319C LYS* 3.4 22.8 + - - +
374C GLY 3.0 22.4 + - - +
375C ASN* 3.2 23.4 + - - +
511C PHE* 4.8 9.3 - - + -
534C ASP* 3.0 21.4 + - - -
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Residues in contact with VAL 316 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
184C GLY* 3.7 21.3 - - - -
185C VAL* 3.9 19.3 - - + +
204C VAL* 6.0 2.9 - - + -
308C LEU* 3.9 14.4 - - + -
312C GLY 3.1 20.2 + - - +
313C ARG* 3.3 27.4 - - - +
315C LYS* 1.3 75.4 - - - +
317C ASN* 1.3 64.3 + - - +
319C LYS* 3.3 4.5 + - - +
320C LEU* 3.0 41.4 + - + +
322C LEU* 6.3 0.2 - - + -
333C LEU* 5.3 3.8 - - + -
337C ASP* 4.7 5.4 - - + +
341C THR* 5.9 0.2 - - - +
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Residues in contact with ASN 317 (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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313C ARG* 2.8 56.1 + - - +
314C TYR* 3.8 9.0 - - + +
315C LYS 3.3 0.2 - - - -
316C VAL* 1.3 75.0 - - - +
318C LYS* 1.3 57.5 + - + +
320C LEU* 4.8 2.0 - - - -
321C GLY* 2.4 40.6 + - - +
322C LEU* 3.5 30.4 + - - +
323C HIS* 4.1 19.0 + - - +
324C VAL* 5.4 4.5 - - - -
326C GLU 5.7 0.8 + - - -
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Residues in contact with LYS 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314C TYR* 3.2 57.3 + - + +
315C LYS* 3.4 29.0 - - + +
317C ASN* 1.3 78.8 - - + +
319C LYS* 1.3 61.0 + - - +
320C LEU 3.4 0.3 + - - -
321C GLY* 3.7 7.5 + - - +
324C VAL* 6.0 9.4 - - + -
363C VAL* 3.8 12.0 - - - +
534C ASP* 3.1 31.1 + - - -
535C GLU* 5.8 4.2 + - - +
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Residues in contact with LYS 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185C VAL* 4.0 18.8 - - + +
187C PHE* 3.5 31.6 - - + -
315C LYS* 3.4 13.9 + - - +
316C VAL 3.3 8.9 + - - +
317C ASN 3.2 0.6 - - - -
318C LYS* 1.3 80.6 - - - +
320C LEU* 1.3 58.5 + - + +
344C TYR* 3.0 52.4 + - - +
363C VAL* 3.2 9.2 - - + +
364C PRO 4.2 5.0 + - - +
366C GLU* 3.3 15.0 + - - +
368C ASP* 2.6 39.1 + - - +
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Residues in contact with LEU 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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185C VAL* 4.9 4.7 - - + -
187C PHE* 5.0 5.4 - - + -
316C VAL* 3.0 33.8 + - + +
317C ASN 4.1 0.9 - - - +
319C LYS* 1.3 78.9 - - + +
321C GLY* 1.3 66.4 + - - +
322C LEU* 3.9 17.7 - - + +
337C ASP* 3.9 16.6 - - - +
340C ALA* 3.4 33.7 - - + +
341C THR* 3.9 21.5 - - - +
344C TYR* 3.7 24.5 - - + -
355C MET* 4.7 0.2 - - - +
357C VAL* 3.4 23.7 - - + +
363C VAL* 3.4 12.1 - - - +
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Residues in contact with GLY 321 (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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317C ASN 2.4 23.6 + - - -
318C LYS* 3.7 5.5 + - - -
319C LYS 3.6 1.6 - - - -
320C LEU* 1.3 73.1 - - - +
322C LEU* 1.3 55.5 + - - +
324C VAL* 4.9 7.4 - - - -
357C VAL* 4.8 0.3 - - - +
360C GLY* 3.1 24.4 - - - -
361C VAL* 3.1 20.2 + - - +
363C VAL* 3.5 15.7 - - - +
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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