Contacts of the helix formed by residues 323 - 341 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319A ASP* 3.2 20.6 - - - -
320A THR 3.2 7.3 + - - -
321A VAL 3.4 1.2 + - - -
322A ASP* 1.3 78.9 - - - +
324A MET* 1.3 65.7 + - - +
326A ALA* 3.1 19.7 + - - +
327A MET* 3.2 17.3 + - - +
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Residues in contact with MET 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277A ALA 3.7 17.5 - - - +
278A PHE* 3.9 10.1 - - - +
280A PRO* 3.7 32.8 - - + -
319A ASP* 3.6 0.2 + - - -
320A THR* 3.1 24.7 + - + +
322A ASP* 3.6 2.4 + - + +
323A GLY* 1.3 75.3 - - - +
325A THR* 1.3 58.4 + - - +
327A MET* 3.0 6.8 + - - +
328A VAL* 2.9 29.0 + - + +
276C PRO* 3.8 35.0 - - + +
277C ALA* 4.2 3.4 - - - -
280C PRO* 4.9 10.5 - - + -
285C ILE* 4.3 24.6 - - + +
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Residues in contact with THR 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A VAL* 3.9 20.9 - - + -
278A PHE 4.9 0.2 - - - -
279A ALA* 4.0 7.4 - - + -
280A PRO* 3.2 14.6 - - - +
281A GLY* 2.9 31.5 + - - +
314A PHE* 3.6 20.9 - - + -
319A ASP* 2.6 31.2 + - - -
324A MET* 1.3 70.2 - - - +
326A ALA* 1.3 56.2 + - - +
328A VAL* 3.2 8.5 + - + +
329A ALA* 2.7 34.0 + - - +
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Residues in contact with ALA 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ARG* 4.2 12.1 - - + +
89A ILE* 4.6 2.8 - - - +
92A ALA* 3.5 16.2 - - + +
314A PHE* 3.5 28.8 - - + -
319A ASP* 3.1 8.8 + - - +
323A GLY* 3.1 14.4 + - - +
325A THR* 1.3 75.9 - - - +
327A MET* 1.3 51.2 + - - +
329A ALA* 3.3 2.6 + - - +
330A ALA* 2.9 34.5 + - - +
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Residues in contact with MET 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ALA* 3.6 30.7 - - - +
95A CYS* 4.4 11.7 - - + -
97A SER* 4.4 4.7 - - - +
98A THR* 3.5 32.1 - - + -
322A ASP 5.3 2.5 - - - +
323A GLY 3.2 13.9 + - - +
324A MET 3.0 8.0 + - - +
326A ALA* 1.3 71.1 - - - +
328A VAL* 1.3 61.0 + - - +
330A ALA* 3.2 3.9 + - + +
331A LYS* 2.9 32.6 + - - +
285C ILE* 3.7 43.1 - - + +
286C GLU* 5.8 0.2 - - - +
287C PRO* 4.0 8.3 - - + +
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Residues in contact with VAL 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A VAL* 4.8 4.7 - - + -
274A LEU* 3.5 30.3 - - + -
278A PHE* 3.4 23.8 - - + +
279A ALA* 4.4 9.2 - - + -
292A PHE* 3.5 12.0 - - + -
324A MET* 2.9 19.4 + - + +
325A THR* 3.4 10.8 - - - +
327A MET* 1.3 78.2 - - - +
329A ALA* 1.3 64.5 + - - +
331A LYS 3.4 0.2 + - - -
332A LEU* 3.2 26.1 + - + +
276C PRO* 5.8 2.0 - - + -
287C PRO* 3.9 24.2 - - + -
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Residues in contact with ALA 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 4.0 27.6 - - + -
271A VAL* 4.4 4.7 - - + -
311A VAL* 4.1 11.6 - - + +
314A PHE* 4.3 14.6 - - + -
325A THR 2.7 18.8 + - - +
326A ALA 3.9 3.6 - - - +
328A VAL* 1.3 70.0 - - - +
330A ALA* 1.3 65.2 + - - +
332A LEU* 3.3 13.5 + - - +
333A VAL* 3.0 26.3 + - - +
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Residues in contact with ALA 330 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A ILE* 3.7 8.8 - - - +
92A ALA* 3.7 10.5 - - + +
93A ILE* 3.6 41.6 - - + +
326A ALA 2.9 17.8 + - - +
327A MET* 3.2 6.7 + - + +
329A ALA* 1.3 76.2 - - - +
331A LYS* 1.3 57.0 + - - +
333A VAL* 3.1 4.0 + - - +
334A ARG* 2.9 34.8 + - - +
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Residues in contact with LYS 331 (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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103A GLU* 2.7 41.8 + - - -
292A PHE* 3.9 19.5 - - + -
296A LEU* 4.3 5.8 - - - -
327A MET 2.9 16.2 + - - +
330A ALA* 1.3 72.1 - - - +
332A LEU* 1.3 60.8 + - - +
334A ARG* 3.7 15.4 - - + +
335A GLU* 2.9 37.8 + - + +
223C ARG* 3.7 11.7 + - - +
286C GLU* 2.9 29.7 + - - +
287C PRO* 2.8 37.4 + - + +
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Residues in contact with LEU 332 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A ILE* 4.0 29.4 - - + -
271A VAL* 4.3 10.3 - - + -
273A CYS* 5.9 0.2 - - - -
274A LEU* 4.6 8.1 - - + -
292A PHE* 3.8 21.5 - - + -
295A VAL* 3.8 29.6 - - + -
296A LEU* 4.9 1.8 - - + -
299A LEU* 4.6 6.0 - - + +
311A VAL* 4.2 22.2 - - + -
328A VAL* 3.2 24.1 + - + +
329A ALA* 3.3 10.3 + - - +
331A LYS* 1.3 72.4 - - - +
333A VAL* 1.3 66.7 + - - +
335A GLU* 4.1 3.3 - - - +
336A LEU* 2.9 30.5 + - - +
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Residues in contact with VAL 333 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A LEU* 3.6 30.5 - - + -
89A ILE* 3.9 10.8 - - + -
93A ILE* 3.8 19.1 - - + -
114A LEU* 5.4 2.0 - - + -
155A LEU* 3.6 10.7 - - + +
157A LEU* 3.6 23.6 - - + -
311A VAL* 4.0 17.3 - - + -
329A ALA 3.0 19.1 + - - +
330A ALA 3.1 7.4 + - - +
332A LEU* 1.3 76.0 - - - +
334A ARG* 1.3 54.0 + - - +
336A LEU* 3.3 3.3 + - - +
337A ALA* 2.8 35.2 + - + +
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Residues in contact with ARG 334 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92A ALA 5.3 0.4 + - - -
93A ILE* 3.1 43.6 + - + +
98A THR* 3.9 11.5 + - - +
99A ASN* 2.8 31.9 + - - +
100A SER* 4.5 1.0 - - - +
101A ALA 2.9 25.1 + - - -
102A THR* 3.6 13.8 - - + +
108A LEU* 3.2 41.3 - - + +
114A LEU* 5.6 1.1 - - + -
330A ALA* 2.9 26.1 + - - +
331A LYS* 3.7 19.1 - - + +
333A VAL* 1.3 73.6 - - + +
335A GLU* 1.3 63.3 + - - +
337A ALA* 3.3 5.8 + - - +
338A ALA* 3.2 22.2 + - - +
286C GLU* 5.7 4.1 + - - -
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Residues in contact with GLU 335 (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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102A THR* 3.5 13.7 + - - +
103A GLU* 2.9 41.9 + - - +
104A GLU* 4.6 2.8 + - - +
296A LEU* 3.9 31.2 - - + -
299A LEU* 5.2 5.6 - - + -
300A HIS* 2.8 31.7 + - + +
331A LYS* 2.9 34.4 + - + +
332A LEU* 4.1 2.7 - - - +
334A ARG* 1.3 70.1 + - - +
336A LEU* 1.3 67.3 + - - +
338A ALA* 3.1 16.4 + - - +
339A LYS* 3.2 13.0 + - - +
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Residues in contact with LEU 336 (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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155A LEU* 3.6 13.2 - - + -
267A ILE* 4.1 32.5 - - + -
269A ILE* 3.8 18.4 - - + -
299A LEU* 4.5 13.8 - - + +
309A ALA* 4.0 23.8 - - + -
310A ASP 4.3 2.5 - - - +
311A VAL* 3.6 31.0 - - + -
332A LEU 2.9 17.4 + - - +
333A VAL 3.4 4.0 - - - +
335A GLU* 1.3 75.3 - - - +
337A ALA* 1.3 62.1 + - - +
339A LYS* 3.1 10.2 + - + +
340A ILE* 2.9 32.5 + - + +
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Residues in contact with ALA 337 (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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65A THR* 3.2 34.1 - - + +
108A LEU* 4.8 7.0 - - + -
113A VAL* 4.0 9.4 - - + +
114A LEU* 4.4 12.1 - - + -
155A LEU* 4.1 0.8 - - + +
333A VAL 2.8 19.5 + - - +
334A ARG* 3.7 9.0 - - - +
335A GLU 3.2 0.4 - - - -
336A LEU* 1.3 72.7 - - - +
338A ALA* 1.3 56.0 + - - +
341A SER* 3.0 36.9 + - - -
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Residues in contact with ALA 338 (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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102A THR* 3.4 30.3 - - + +
104A GLU* 4.8 14.8 - - + +
106A LYS* 3.1 41.8 + - + +
113A VAL* 5.2 1.8 - - - +
334A ARG 3.2 10.8 + - - +
335A GLU* 3.1 15.6 + - - +
337A ALA* 1.3 76.0 - - - +
339A LYS* 1.3 58.3 + - - +
341A SER* 5.2 0.2 - - - -
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Residues in contact with LYS 339 (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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104A GLU* 5.8 2.0 - - - +
267A ILE* 4.7 8.3 - - + -
299A LEU* 2.5 36.0 + - + +
300A HIS* 3.9 10.4 + - + +
302A LEU* 2.5 49.5 + - - +
304A ALA 5.0 4.0 - - - +
306A VAL* 4.1 23.0 + - + +
335A GLU 3.2 10.1 + - - +
336A LEU* 3.1 13.8 + - + +
338A ALA* 1.3 79.7 - - - +
340A ILE* 1.3 64.2 + - + +
341A SER 3.8 4.0 - - - +
342A LYS* 4.9 7.4 + - - +
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Residues in contact with ILE 340 (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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63A ALA* 3.1 18.6 - - + +
65A THR* 3.4 21.3 - - + +
153A ARG* 3.7 31.0 - - + +
154A PRO 5.1 1.6 - - - +
155A LEU* 4.3 15.0 - - + -
306A VAL* 3.6 39.7 - - + +
307A VAL 5.4 0.4 - - - -
308A GLY* 4.6 5.8 - - - +
309A ALA* 3.9 26.9 - - + -
336A LEU* 2.9 24.5 + - + +
339A LYS* 1.3 77.0 - - + +
341A SER* 1.3 63.8 + - - +
342A LYS* 4.1 7.4 + - - +
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Residues in contact with SER 341 (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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63A ALA 3.1 12.8 - - - -
65A THR* 2.7 23.2 + - - -
106A LYS* 2.7 27.9 + - - -
112A ARG 3.7 8.7 - - - -
113A VAL* 2.4 37.6 + - - -
337A ALA 3.0 10.4 + - - -
338A ALA 3.7 3.5 - - - +
339A LYS 3.8 3.6 - - - +
340A ILE* 1.3 77.9 - - - +
342A LYS* 1.3 59.8 + - - +
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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