Contacts of the helix formed by residues 311 - 326 (chain A) in PDB entry 4UHW
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 311 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ARG* 3.6 11.3 + - - -
309A GLY 3.7 2.0 + - - -
310A LEU* 1.3 76.9 - - - +
312A LEU* 1.3 64.2 + - - +
313A ALA* 3.5 4.7 + - - +
314A GLN* 3.1 36.8 + - - +
315A VAL* 3.1 22.3 + - - +
350A ARG 3.6 11.0 - - - -
351A ASN 3.6 17.3 - - - -
352A MET 4.9 1.6 - - - -
353A ALA 3.1 10.5 - - - -
354A SER* 4.2 0.7 - - - +
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Residues in contact with LEU 312 (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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311A SER* 1.3 73.1 - - - +
313A ALA* 1.3 57.8 + - - +
315A VAL* 3.4 7.2 + - + +
316A LYS* 3.0 27.0 + - - +
341A LEU* 4.1 14.7 - - + +
344A LEU* 3.7 35.0 - - + -
350A ARG* 3.2 15.5 + - + +
353A ALA* 2.8 37.8 + - + +
354A SER 3.9 14.6 - - - +
355A LEU* 4.0 20.4 - - + -
358A HIS* 4.3 4.0 - - + +
368A LEU* 4.0 20.2 - - + -
3006A FAD 4.0 11.2 - - - +
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Residues in contact with ALA 313 (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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311A SER* 3.7 4.7 - - - +
312A LEU* 1.3 76.7 - - - +
314A GLN* 1.3 62.4 + - + +
316A LYS* 3.1 18.9 + - - +
317A ASP* 3.1 20.7 + - - +
350A ARG* 3.0 21.0 + - + +
351A ASN* 3.5 38.6 - - - +
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Residues in contact with GLN 314 (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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67A ARG* 3.3 41.9 + - - +
290A ARG* 5.0 10.8 + - - +
309A GLY 4.8 0.5 - - - +
310A LEU* 3.6 20.5 - - + +
311A SER* 3.1 38.3 + - - +
313A ALA* 1.3 72.1 - - + +
315A VAL* 1.3 59.6 + - - +
317A ASP* 3.4 11.5 + - - +
318A ILE* 3.0 40.0 + - + +
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Residues in contact with VAL 315 (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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306A LEU* 4.0 19.5 - - + -
310A LEU* 4.0 26.2 - - + -
311A SER 3.1 19.2 + - - +
312A LEU* 3.6 10.8 - - + +
313A ALA 3.3 0.4 - - - -
314A GLN* 1.3 73.6 - - - +
316A LYS* 1.3 66.1 + - - +
318A ILE* 3.5 5.9 + - - +
319A LEU* 3.1 43.0 + - + +
337A LEU* 6.1 0.9 - - + -
341A LEU* 4.0 11.7 - - + -
355A LEU* 4.3 26.2 - - + -
368A LEU* 6.5 0.4 - - + -
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Residues in contact with LYS 316 (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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142A ASP* 5.8 3.8 + - - -
312A LEU 3.0 13.5 + - - +
313A ALA* 3.1 12.1 + - - +
315A VAL* 1.3 77.8 - - - +
317A ASP* 1.3 60.3 + - - +
319A LEU* 3.9 2.8 - - - +
320A ALA* 3.1 29.0 + - - +
338A LEU* 4.2 19.4 - - + +
341A LEU* 3.5 50.5 - - + +
342A GLY* 3.9 10.0 - - - +
350A ARG* 4.2 20.9 - - - +
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Residues in contact with ASP 317 (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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313A ALA* 3.1 16.8 + - - +
314A GLN* 3.7 10.9 - - - +
315A VAL 3.2 0.4 - - - -
316A LYS* 1.3 78.9 + - - +
318A ILE* 1.3 66.4 + - + +
320A ALA* 3.3 7.1 + - - +
321A ASP* 3.2 23.6 + - - +
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Residues in contact with ILE 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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297A VAL* 3.6 41.1 - - + -
299A HIS* 5.1 2.0 - - + -
304A LEU* 4.5 11.9 - - + -
306A LEU* 3.9 21.1 - - + -
310A LEU* 4.1 20.6 - - + -
314A GLN* 3.0 28.1 + - + +
315A VAL* 3.8 6.5 - - - +
317A ASP* 1.3 77.2 - - + +
319A LEU* 1.3 62.0 + - + +
321A ASP* 3.4 5.0 + - - +
322A VAL* 3.1 34.7 + - + +
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Residues in contact with LEU 319 (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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304A LEU* 4.3 17.0 - - + -
306A LEU* 4.5 14.1 - - + -
315A VAL* 3.1 35.9 + - + +
316A LYS 4.1 0.2 - - - +
318A ILE* 1.3 76.0 - - + +
320A ALA* 1.3 60.1 + - - +
321A ASP 3.3 0.2 - - - -
322A VAL* 4.0 3.5 - - + +
323A VAL* 3.0 33.6 + - - +
334A TYR* 3.8 36.6 - - + +
337A LEU* 3.7 35.7 - - + -
338A LEU* 3.3 16.2 - - + -
341A LEU* 4.4 6.5 - - + -
416A ILE* 5.9 0.4 - - + -
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Residues in contact with ALA 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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316A LYS* 3.1 18.6 + - + +
317A ASP* 3.3 10.1 + - - +
319A LEU* 1.3 76.2 - - - +
321A ASP* 1.3 61.2 + - - +
323A VAL* 3.7 5.0 + - - +
324A GLN* 3.4 26.5 + - - +
338A LEU* 3.5 19.5 - - + +
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Residues in contact with ASP 321 (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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317A ASP 3.2 9.8 + - - +
318A ILE* 3.6 9.4 - - - +
320A ALA* 1.3 76.9 - - - +
322A VAL* 1.3 60.4 + - + +
324A GLN* 3.2 6.2 + - - -
325A LYS* 3.0 60.6 + - - +
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Residues in contact with VAL 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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299A HIS* 3.9 29.4 - - + +
304A LEU* 4.0 18.2 - - + -
318A ILE* 3.1 23.1 + - + +
319A LEU* 4.0 6.3 - - - +
321A ASP* 1.3 75.4 - - + +
323A VAL* 1.3 62.5 + - - +
325A LYS* 3.2 5.1 + - - +
326A LEU* 3.0 44.8 + - + +
331A THR* 4.7 0.7 - - + -
334A TYR* 3.7 34.5 - - + -
418A TYR* 5.2 1.1 - - + -
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Residues in contact with VAL 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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319A LEU 3.0 25.1 + - - +
320A ALA* 3.7 8.3 - - - +
322A VAL* 1.3 76.3 - - - +
324A GLN* 1.3 67.1 + - + +
326A LEU 3.3 17.0 - - - +
328A GLU* 5.8 1.4 - - - +
331A THR* 4.1 12.5 + - - +
334A TYR* 4.0 24.5 - - + -
335A HIS* 3.3 44.4 - - + +
338A LEU* 4.2 12.6 - - + -
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Residues in contact with GLN 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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320A ALA 3.4 13.2 + - - +
321A ASP* 3.2 8.7 + - - +
323A VAL* 1.3 84.9 - - + +
325A LYS* 1.3 75.8 + - + +
326A LEU 3.5 2.2 + - - +
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Residues in contact with LYS 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 ASP* 3.0 43.7 + - - +
322A VAL* 3.2 5.1 + - - +
324A GLN* 1.3 90.0 - - + +
326A LEU* 1.3 71.7 + - + +
327A PRO* 4.8 0.3 - - - +
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Residues in contact with LEU 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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322A VAL* 3.0 32.7 + - + +
323A VAL 3.3 16.6 - - - +
324A GLN 4.4 3.0 - - - +
325A LYS* 1.3 93.5 - - + +
327A PRO* 1.4 73.2 - - + +
328A GLU* 4.0 0.9 + - - +
330A LYS* 4.7 11.0 - - + +
331A THR* 3.5 14.3 - - + +
418A TYR* 3.4 44.9 - - + +
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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