Contacts of the helix formed by residues 317 - 333 (chain X) in PDB entry 1UL1
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 317 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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311X CYS* 3.7 0.2 - - - -
316X PHE* 1.3 66.7 - - - +
318X GLU* 1.3 63.6 + - - +
319X GLU* 3.4 20.4 + - - +
320X ARG* 3.0 43.0 + - - +
321X ILE* 3.1 16.1 + - - +
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Residues in contact with GLU 318 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307X ILE* 3.9 25.3 - - + +
311X CYS* 3.2 18.6 - - + +
316X PHE 3.1 5.1 + - - -
317X SER* 1.3 71.6 + - - +
319X GLU* 1.3 61.8 + - - +
321X ILE 4.1 0.4 - - - -
322X ARG* 2.8 64.8 + - + +
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Residues in contact with GLU 319 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317X SER* 3.0 11.5 + - - +
318X GLU* 1.3 80.3 - - - +
320X ARG* 1.3 61.0 + - + +
322X ARG* 4.0 3.3 - - - +
323X SER* 3.0 28.8 + - - -
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Residues in contact with ARG 320 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65X MET* 5.2 2.8 - - - +
69X TYR* 3.3 42.3 + - - +
316X PHE* 3.5 28.3 - - - -
317X SER* 3.0 42.9 + - - +
319X GLU* 1.3 79.4 - - + +
321X ILE* 1.3 68.9 + - - +
323X SER* 2.8 20.3 + - - -
324X GLY* 2.9 12.6 + - - -
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Residues in contact with ILE 321 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X PHE* 4.1 19.5 - - + -
69X TYR* 4.5 2.2 - - - +
306X LEU* 4.7 1.8 - - + +
307X ILE* 4.5 14.4 - - + +
310X MET* 3.6 28.7 - - + -
311X CYS* 3.4 23.3 - - - -
316X PHE* 3.6 16.6 - - + -
317X SER 3.1 14.4 + - - +
320X ARG* 1.3 97.8 - - - +
322X ARG* 1.3 59.4 + - - +
324X GLY 3.2 0.5 + - - -
325X VAL* 2.7 56.5 + - + +
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Residues in contact with ARG 322 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303X GLU* 3.0 22.6 + - - -
307X ILE* 2.8 39.7 - - + +
318X GLU* 2.8 58.7 + - + +
319X GLU* 4.0 3.6 - - - +
321X ILE* 1.3 77.7 - - + +
323X SER* 1.3 63.4 + - - +
325X VAL* 3.5 7.4 - - - +
326X LYS* 3.0 21.0 + - - +
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Residues in contact with SER 323 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319X GLU 3.0 13.9 + - - -
320X ARG* 2.8 23.9 + - - -
322X ARG* 1.3 76.4 - - - +
324X GLY* 1.3 68.2 + - - +
326X LYS* 2.9 23.1 + - - +
327X ARG* 3.1 10.4 + - - +
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Residues in contact with GLY 324 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X PHE* 4.8 4.5 - - - -
69X TYR* 4.8 4.7 - - - -
72X ILE* 3.7 20.0 - - - +
320X ARG 2.9 9.6 + - - -
321X ILE 3.7 1.8 - - - -
323X SER* 1.3 80.7 + - - +
325X VAL* 1.3 55.4 + - - +
327X ARG* 2.7 42.0 + - - +
328X LEU 3.0 8.7 + - - -
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Residues in contact with VAL 325 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68X PHE* 3.9 10.5 - - + -
72X ILE* 4.8 0.4 - - - -
301X PRO* 5.2 6.7 - - + -
303X GLU* 4.2 32.3 - - + +
306X LEU* 3.8 30.3 - - + -
307X ILE* 5.4 2.2 - - + -
321X ILE* 2.7 50.3 + - + +
322X ARG* 3.5 7.6 - - - +
324X GLY* 1.3 69.8 - - - +
326X LYS* 1.3 62.2 + - - +
328X LEU* 3.4 10.7 + - - +
329X SER* 3.1 24.1 + - - -
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Residues in contact with LYS 326 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322X ARG 3.0 13.1 + - - +
323X SER* 2.9 18.7 + - - +
324X GLY 2.8 1.0 + - - -
325X VAL* 1.3 75.3 - - - +
327X ARG* 1.3 66.4 + - + +
328X LEU 3.1 0.5 + - - -
329X SER* 3.2 4.4 + - - -
330X LYS* 3.2 19.2 + - - +
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Residues in contact with ARG 327 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69X TYR* 3.8 27.7 + - - +
70X ARG* 6.1 0.6 - - - +
72X ILE* 3.3 33.1 - - + +
73X ARG* 4.8 4.6 - - - +
76X GLU* 2.9 42.6 + - - +
323X SER 3.8 9.4 - - - +
324X GLY* 2.7 18.0 + - - +
326X LYS* 1.3 74.0 - - + +
328X LEU* 1.3 65.7 + - - +
330X LYS* 3.0 25.1 + - - +
331X SER* 3.3 8.0 + - - -
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Residues in contact with LEU 328 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68X PHE* 5.7 0.4 - - + -
72X ILE* 4.3 16.3 - - + +
75X MET* 3.6 40.4 - - + -
148X MET* 3.7 36.3 - - + -
150X ILE* 4.8 4.7 - - + -
301X PRO* 3.5 32.3 - - + -
306X LEU* 5.0 5.4 - - + -
324X GLY 3.0 9.7 + - - +
325X VAL* 3.5 12.6 - - - +
326X LYS 3.1 0.2 - - - -
327X ARG* 1.3 75.8 - - - +
329X SER* 1.3 58.6 + - - +
330X LYS 2.9 0.9 + - - -
331X SER* 3.1 7.0 + - - -
332X ARG* 2.9 31.1 + - + +
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Residues in contact with SER 329 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300X GLU* 5.8 1.0 - - - +
301X PRO* 4.6 14.9 - - - +
325X VAL* 3.1 14.8 + - - -
326X LYS* 3.2 4.2 + - - -
328X LEU* 1.3 78.5 - - - +
330X LYS* 1.3 59.0 + - - +
332X ARG* 3.4 22.9 - - - +
333X GLN* 3.4 18.4 + - - +
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Residues in contact with LYS 330 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326X LYS 3.2 10.5 + - - +
327X ARG* 3.0 15.2 + - - +
328X LEU 2.9 1.0 + - - -
329X SER* 1.3 75.1 - - - +
331X SER* 1.3 69.2 + - - +
332X ARG 3.1 0.9 - - - -
333X GLN* 3.2 30.5 + - - +
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Residues in contact with SER 331 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75X MET* 3.6 26.5 - - - +
76X GLU* 3.5 33.5 + - - +
327X ARG 3.3 6.5 + - - -
328X LEU* 3.1 9.0 + - - -
330X LYS* 1.3 80.0 - - - +
332X ARG* 1.3 77.3 + - - +
333X GLN 2.7 16.3 + - - +
334X GLY* 3.5 3.3 + - - -
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Residues in contact with ARG 332 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A GLU 5.1 1.2 + - - -
259A GLU* 2.8 39.6 + - - +
75X MET* 4.8 12.3 - - - -
298X TRP* 3.4 28.5 + - - +
299X SER 3.8 11.1 + - - -
300X GLU* 3.2 36.7 + - + +
301X PRO* 4.1 11.0 - - + -
328X LEU* 2.9 21.1 + - + +
329X SER* 3.4 23.1 - - - +
331X SER* 1.3 81.3 + - - +
333X GLN* 1.3 57.1 + - + +
334X GLY* 2.6 19.4 + - - -
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Residues in contact with GLN 333 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329X SER* 3.4 16.2 + - - +
330X LYS* 3.2 22.7 - - - +
331X SER 2.7 10.3 + - - +
332X ARG* 1.3 73.6 - - + +
334X GLY* 1.3 63.7 + - - +
335X SER* 3.5 3.8 + - - -
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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
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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