Contacts of the helix formed by residues 317 - 331 (chain A) in PDB entry 1UWV
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 VAL 317 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A GLU* 3.0 19.7 + - - +
316A GLY* 1.3 80.8 - - - +
318A PRO* 1.3 71.8 - - + +
319A ALA* 3.8 17.3 - - + +
320A LEU* 3.1 33.4 + - + +
321A VAL* 3.1 10.4 + - - +
340A HIS* 3.9 2.5 - - - -
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Residues in contact with PRO 318 (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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316A GLY 3.7 1.8 - - - +
317A VAL* 1.3 88.4 - - + +
319A ALA* 1.3 63.1 + - - +
321A VAL* 3.0 8.1 + - + +
322A GLU* 3.0 39.6 + - - +
340A HIS* 3.6 31.4 - - + +
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Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A ASP* 4.9 13.9 - - - +
317A VAL* 3.3 11.1 - - + +
318A PRO* 1.3 78.9 - - - +
320A LEU* 1.3 62.6 + - + +
322A GLU* 3.6 11.4 + - - +
323A LYS* 3.2 22.7 + - - +
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Residues in contact with LEU 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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262A ASP* 4.8 22.0 - - + +
263A PHE* 4.9 18.8 - - + +
296A GLY* 3.6 21.8 - - - +
297A MSE 3.5 31.6 - - + +
315A GLU* 3.5 24.9 - - + +
317A VAL* 3.1 27.8 + - + +
319A ALA* 1.3 77.1 - - + +
321A VAL* 1.3 65.9 + - - +
323A LYS* 4.6 1.1 - - + -
324A GLY* 3.0 19.1 + - - -
338A PHE* 5.3 0.2 - - - -
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Residues in contact with VAL 321 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A CYS* 5.8 0.2 - - - -
296A GLY 4.8 1.8 - - - -
315A GLU* 3.8 21.8 - - + +
317A VAL 3.1 14.9 + - - +
318A PRO* 3.0 10.8 + - + +
320A LEU* 1.3 77.2 - - - +
322A GLU* 1.3 65.2 + - + +
324A GLY* 3.4 1.2 + - - -
325A GLN* 3.1 35.7 + - - +
338A PHE* 3.8 31.8 - - + +
339A TYR 3.7 21.3 - - - +
340A HIS* 3.9 15.0 - - + +
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Residues in contact with GLU 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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318A PRO* 3.0 30.0 + - + +
319A ALA* 3.9 8.8 + - - +
321A VAL* 1.3 79.1 - - + +
323A LYS* 1.3 56.7 + - - +
325A GLN* 3.4 17.0 + - - +
326A GLN* 3.0 36.7 + - - +
329A ARG* 5.1 0.3 + - - -
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Residues in contact with LYS 323 (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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246A MSE 4.2 18.2 - - - -
257A THR* 3.4 31.5 + - - +
258A PHE* 4.0 2.2 - - - +
259A SER* 4.0 16.6 - - - +
262A ASP* 3.6 23.1 - - - +
297A MSE 3.7 22.2 - - + -
319A ALA 3.2 16.8 + - - +
320A LEU* 3.9 5.6 - - + +
321A VAL 3.3 0.4 - - - -
322A GLU* 1.3 74.6 - - - +
324A GLY* 1.3 60.3 + - - +
326A GLN* 3.1 28.1 + - + +
327A ASN* 2.8 30.9 + - - +
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Residues in contact with GLY 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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297A MSE 3.4 23.6 + - - -
302A LEU* 4.1 1.2 - - - +
320A LEU 3.0 13.2 + - - -
321A VAL 3.7 4.0 - - - -
322A GLU 3.4 0.2 - - - -
323A LYS* 1.3 76.1 - - - +
325A GLN* 1.3 54.9 + - - +
327A ASN* 3.4 2.1 + - - +
328A ALA* 2.9 24.6 + - - +
338A PHE* 3.4 28.5 - - - -
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Residues in contact with GLN 325 (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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321A VAL* 3.1 24.9 + - - +
322A GLU* 3.6 19.5 - - - +
323A LYS 3.3 0.4 - - - -
324A GLY* 1.3 71.7 - - - +
326A GLN* 1.3 64.2 + - - +
328A ALA* 3.5 5.4 + - - +
329A ARG* 3.2 42.6 + - - +
337A THR* 5.8 1.6 - - - +
338A PHE* 3.5 38.9 + - + +
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Residues in contact with GLN 326 (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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257A THR* 4.5 4.7 + - - +
322A GLU* 3.0 20.4 + - - +
323A LYS* 3.1 40.8 + - + +
325A GLN* 1.3 75.1 - - - +
327A ASN* 1.3 62.2 + - - +
329A ARG* 3.2 28.7 + - - +
330A LEU* 3.0 34.2 + - + +
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Residues in contact with ASN 327 (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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255A ARG 4.3 1.0 - - - +
256A LEU* 3.8 10.5 - - + +
257A THR* 2.7 58.9 + - - +
297A MSE 3.5 23.8 + - - +
302A LEU* 3.7 19.5 - - + -
323A LYS* 2.8 22.0 + - - +
324A GLY* 4.0 0.4 - - - +
326A GLN* 1.3 73.3 - - - +
328A ALA* 1.3 67.0 + - - +
330A LEU* 3.5 7.1 + - - +
331A ASN* 2.9 31.0 + - - +
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Residues in contact with ALA 328 (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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302A LEU* 3.9 9.5 - - + +
324A GLY 2.9 17.9 + - - +
325A GLN* 3.6 8.7 - - - +
327A ASN* 1.3 75.7 - - - +
329A ARG* 1.3 60.8 + - + +
331A ASN 3.2 1.4 + - - -
332A GLY 3.1 4.3 + - - -
333A LEU* 2.9 41.9 + - - +
336A VAL* 3.7 31.2 - - + +
338A PHE* 4.5 1.6 - - + -
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Residues in contact with ARG 329 (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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322A GLU 5.1 0.4 + - - -
325A GLN* 3.2 27.7 + - - +
326A GLN* 3.2 37.2 + - - +
328A ALA* 1.3 78.2 - - + +
330A LEU* 1.3 65.0 + - - +
332A GLY* 3.1 13.4 + - - -
333A LEU 5.0 2.7 - - - +
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Residues in contact with LEU 330 (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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255A ARG 5.0 3.1 - - - +
257A THR* 3.5 36.3 - - + +
326A GLN* 3.0 18.5 + - + +
327A ASN* 3.8 10.5 - - - +
328A ALA 3.4 0.2 - - - -
329A ARG* 1.3 78.0 - - + +
331A ASN* 1.3 63.5 + - - +
332A GLY 3.5 0.6 + - - -
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Residues in contact with ASN 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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253A GLY 4.8 0.5 - - - +
254A LEU* 3.6 21.1 - - + +
255A ARG* 2.8 48.6 + - - +
256A LEU* 4.3 8.1 - - - +
302A LEU* 5.2 1.0 - - - +
327A ASN 2.9 29.4 + - - +
329A ARG 3.1 0.4 - - - -
330A LEU* 1.3 79.8 - - - +
332A GLY* 1.3 63.4 + - - +
333A LEU* 3.3 26.0 + - + +
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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
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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