Contacts of the helix formed by residues 323 - 341 (chain C) in PDB entry 6VSU
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 GLY 323 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319C ASP* 3.2 18.6 - - - -
320C THR 3.2 9.3 + - - -
321C VAL 3.5 0.6 - - - -
322C ASP* 1.3 79.7 - - - +
324C MET* 1.3 65.4 + - - +
326C ALA* 3.0 20.0 + - - +
327C MET* 3.2 15.7 + - - +
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Residues in contact with MET 324 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B PRO* 3.7 39.0 - - + +
277B ALA* 4.1 2.0 - - - -
280B PRO* 4.6 11.0 - - + -
285B ILE* 4.3 25.2 - - + +
277C ALA 3.8 13.2 - - - +
278C PHE 3.8 13.5 - - - +
280C PRO* 3.6 33.2 - - + -
319C ASP* 3.6 0.6 + - - -
320C THR* 3.1 24.9 + - + +
322C ASP* 3.6 2.6 - - + -
323C GLY* 1.3 75.1 - - - +
325C THR* 1.3 57.1 + - - +
327C MET* 3.1 6.8 + - - +
328C VAL* 3.1 26.9 + - + +
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Residues in contact with THR 325 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271C VAL* 3.8 21.5 - - + -
279C ALA* 3.7 8.2 - - + -
280C PRO* 3.2 16.6 - - - +
281C GLY 3.0 38.9 + - - +
314C PHE* 3.7 11.0 - - + -
319C ASP* 2.9 25.4 + - - -
324C MET* 1.3 72.6 - - - +
326C ALA* 1.3 55.9 + - - +
328C VAL* 3.2 7.9 + - + +
329C ALA* 2.8 33.3 + - - +
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Residues in contact with ALA 326 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88C ARG* 4.2 11.7 - - + +
89C ILE* 4.7 2.4 - - - -
92C ALA* 3.3 16.3 - - + +
314C PHE* 3.4 29.8 - - + -
319C ASP* 3.1 8.3 + - - +
323C GLY* 3.0 15.5 + - - +
325C THR* 1.3 77.8 - - - +
327C MET* 1.3 56.3 + - - +
329C ALA* 3.5 2.3 + - - +
330C ALA* 2.9 27.9 + - - +
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Residues in contact with MET 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285B ILE* 3.9 41.7 - - + +
287B PRO* 3.9 8.8 - - + +
92C ALA* 3.6 29.6 - - + +
95C CYS* 4.3 15.3 - - - -
97C SER* 4.8 2.5 - - - +
98C THR* 3.6 29.8 - - + -
322C ASP 5.4 2.7 - - - +
323C GLY 3.2 14.1 + - - +
324C MET 3.1 7.2 + - - +
326C ALA* 1.3 74.1 - - + +
328C VAL* 1.3 60.4 + - - +
330C ALA* 3.7 3.2 - - + +
331C LYS* 2.9 31.3 + - + +
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Residues in contact with VAL 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B PRO* 6.3 0.4 - - + -
287B PRO* 3.9 22.2 - - + -
271C VAL* 5.0 3.1 - - + -
274C LEU* 3.4 32.5 - - + -
278C PHE* 3.4 25.4 - - + +
279C ALA* 4.5 6.1 - - + -
292C PHE* 3.5 12.6 - - + -
324C MET* 3.1 16.7 + - + +
325C THR* 3.3 13.9 - - + +
327C MET* 1.3 74.0 - - - +
329C ALA* 1.3 65.7 + - - +
331C LYS 3.3 1.2 + - - -
332C LEU* 3.1 29.2 + - + +
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Residues in contact with ALA 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ILE* 3.8 31.2 - - + -
271C VAL* 4.5 4.3 - - + -
311C VAL* 4.3 16.5 - - + +
314C PHE* 4.1 14.6 - - + -
325C THR 2.8 18.7 + - - +
326C ALA 3.9 4.0 - - - +
328C VAL* 1.3 71.2 - - - +
330C ALA* 1.3 62.9 + - - +
332C LEU* 3.1 7.7 + - - +
333C VAL* 2.9 26.2 + - - +
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Residues in contact with ALA 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C ILE* 3.9 13.2 - - - +
92C ALA* 3.4 23.8 - - + +
93C ILE* 3.6 23.1 - - + +
326C ALA 2.9 19.8 + - - +
327C MET* 3.7 6.5 - - + +
328C VAL 3.2 0.4 - - - -
329C ALA* 1.3 76.2 - - - +
331C LYS* 1.3 59.3 + - - +
333C VAL* 3.2 3.6 + - - +
334C ARG* 2.9 32.7 + - - +
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Residues in contact with LYS 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B ARG* 3.5 11.1 + - - +
286B GLU* 2.8 29.4 + - - +
287B PRO* 3.1 31.1 + - + +
103C GLU* 2.7 39.0 + - - -
292C PHE* 3.6 20.0 - - + -
296C LEU* 4.2 7.9 - - - -
327C MET* 2.9 19.0 + - + +
328C VAL 4.0 0.2 - - - +
329C ALA 3.2 0.2 - - - -
330C ALA* 1.3 78.7 - - - +
332C LEU* 1.3 56.4 + - - +
334C ARG* 3.4 17.9 + - - +
335C GLU* 3.0 36.3 + - + +
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Residues in contact with LEU 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269C ILE* 4.4 22.4 - - + -
271C VAL* 4.6 10.5 - - + -
273C CYS* 6.1 0.4 - - - -
274C LEU* 4.4 9.2 - - + -
292C PHE* 3.6 21.5 - - + -
295C VAL* 3.7 29.6 - - + -
296C LEU* 4.6 2.9 - - + -
299C LEU* 4.5 10.2 - - + +
311C VAL* 4.5 11.2 - - + -
328C VAL* 3.1 35.6 + - + +
329C ALA* 3.1 9.6 + - - +
331C LYS* 1.3 71.9 - - - +
333C VAL* 1.3 57.5 + - - +
335C GLU* 4.2 3.2 - - - +
336C LEU* 2.8 42.6 + - - +
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Residues in contact with VAL 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C LEU* 3.7 28.7 - - + -
89C ILE* 3.9 9.6 - - + -
93C ILE* 3.9 19.1 - - + -
114C LEU* 5.3 3.4 - - + -
155C LEU* 3.5 12.0 - - + +
157C LEU* 3.4 25.6 - - + -
311C VAL* 3.8 18.6 - - + -
329C ALA 2.9 16.9 + - - +
330C ALA 3.4 8.1 - - - +
332C LEU* 1.3 78.0 - - - +
334C ARG* 1.3 53.1 + - + +
336C LEU* 3.3 0.8 + - - -
337C ALA* 2.8 34.3 + - + +
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Residues in contact with ARG 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286B GLU* 5.8 1.6 + - - -
92C ALA 5.2 0.6 + - - -
93C ILE* 3.0 43.8 + - + +
98C THR* 3.9 12.6 + - - +
99C ASN* 2.7 31.9 + - - +
100C SER* 4.6 1.0 - - - +
101C ALA 3.0 24.2 + - - -
102C THR* 3.8 13.7 - - + +
108C LEU* 3.3 40.4 - - + +
114C LEU* 5.9 1.1 - - + -
330C ALA* 2.9 23.3 + - - +
331C LYS* 3.6 21.6 - - + +
332C LEU 3.3 0.2 - - - -
333C VAL* 1.3 76.1 - - + +
335C GLU* 1.3 61.8 + - + +
337C ALA* 3.2 5.7 + - - +
338C ALA* 3.0 25.8 + - - +
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Residues in contact with GLU 335 (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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102C THR* 3.4 12.4 - - - +
103C GLU* 2.8 41.6 + - - +
104C GLU* 4.3 7.6 - - - +
296C LEU* 3.9 27.6 - - + -
299C LEU* 5.0 6.7 - - + -
300C HIS* 2.8 30.8 + - + +
331C LYS* 3.0 32.1 + - + +
332C LEU* 4.2 2.5 - - - +
334C ARG* 1.3 75.4 + - + +
336C LEU* 1.3 66.4 + - - +
338C ALA* 3.0 15.0 + - - +
339C LYS* 3.1 13.7 + - - +
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Residues in contact with LEU 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155C LEU* 3.8 12.1 - - + -
267C ILE* 3.9 36.6 - - + -
269C ILE* 3.7 23.1 - - + -
299C LEU* 4.2 13.6 - - + +
309C ALA* 4.0 21.1 - - + -
310C ASP 4.1 0.9 - - - +
311C VAL* 3.6 31.2 - - + -
332C LEU 2.8 19.0 + - - +
333C VAL 3.5 4.3 - - - +
335C GLU* 1.3 76.7 - - - +
337C ALA* 1.3 55.1 + - - +
339C LYS* 3.4 8.1 + - + +
340C ILE* 3.0 37.6 + - + +
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Residues in contact with ALA 337 (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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65C THR* 3.5 33.2 - - + -
108C LEU* 4.9 5.2 - - + -
113C VAL* 3.9 9.8 - - - +
114C LEU* 4.5 11.7 - - + -
155C LEU* 4.0 0.6 - - + +
333C VAL* 2.8 18.0 + - + +
334C ARG* 3.5 8.1 - - - +
336C LEU* 1.3 76.5 - - - +
338C ALA* 1.3 59.7 + - - +
341C SER* 2.7 36.3 + - - -
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Residues in contact with ALA 338 (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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102C THR* 3.6 28.3 - - + +
104C GLU* 4.3 16.9 - - + +
106C LYS* 3.0 45.9 + - + -
113C VAL* 5.2 2.6 - - - +
334C ARG 3.0 11.9 + - - +
335C GLU* 3.0 11.2 + - - +
337C ALA* 1.3 76.6 - - - +
339C LYS* 1.3 58.2 + - - +
341C SER* 3.5 0.8 - - - +
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Residues in contact with LYS 339 (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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104C GLU* 5.3 1.3 + - - -
267C ILE* 4.5 10.5 - - + -
299C LEU* 3.0 32.9 + - + +
300C HIS* 3.9 10.9 + - - +
302C LEU* 2.8 42.7 + - - -
303C GLN* 4.8 4.8 + - - -
304C ALA* 5.2 4.0 - - - +
306C VAL* 4.2 24.7 + - + +
335C GLU 3.1 10.7 + - - +
336C LEU* 3.6 12.1 - - + +
337C ALA 3.2 0.2 - - - -
338C ALA* 1.3 77.5 - - - +
340C ILE* 1.3 64.1 + - + +
341C SER 3.8 3.0 - - - +
342C LYS* 5.4 4.2 - - - +
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Residues in contact with ILE 340 (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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63C ALA* 3.4 15.5 - - + +
65C THR* 3.0 24.9 - - - +
153C ARG* 3.6 30.7 - - + +
154C PRO 4.7 2.9 - - - +
155C LEU* 4.3 17.0 - - + -
306C VAL* 3.7 38.4 - - + +
307C VAL 5.5 0.7 - - - -
308C GLY* 4.8 1.1 - - - -
309C ALA* 3.6 35.4 - - + +
336C LEU* 3.0 24.9 + - + +
337C ALA 3.5 0.2 + - - -
339C LYS* 1.3 74.8 - - + +
341C SER* 1.3 65.5 + - - +
342C LYS* 3.4 8.7 + - - +
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Residues in contact with SER 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ALA 3.4 10.1 - - - -
65C THR* 3.1 13.3 + - - +
106C LYS* 3.1 24.9 + - - -
112C ARG 3.7 14.4 - - - -
113C VAL* 2.4 37.9 + - - -
337C ALA 2.7 17.2 + - - -
338C ALA 3.5 5.2 - - - +
339C LYS 3.8 3.1 - - - +
340C ILE* 1.3 79.1 - - - +
342C LYS* 1.3 61.8 + - - +
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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