Contacts of the helix formed by residues 313 - 328 (chain A) in PDB entry 1DT6
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 HIS 313 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A LEU* 2.8 20.8 + - + +
310A LEU 3.3 6.1 - - - +
312A LYS* 1.3 109.2 + - + +
314A PRO* 1.3 65.3 - - - +
315A GLU* 3.0 28.9 + - - +
316A VAL* 3.1 25.9 + - + +
317A ALA 3.8 0.7 + - - -
404A PHE* 4.0 38.2 + + + +
466A ILE* 5.9 1.0 - - - +
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Residues in contact with PRO 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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310A LEU 3.2 13.4 - - - +
311A LEU* 3.4 14.8 - - - +
312A LYS 3.7 4.0 - - - +
313A HIS* 1.3 82.7 - - - +
315A GLU* 1.3 67.0 + - - +
316A VAL 3.1 0.2 - - - -
317A ALA* 3.2 6.6 + - + +
318A ALA* 3.0 24.5 + - - +
455A LEU 5.9 2.7 - - - +
461A PRO* 4.3 15.7 - - + -
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Residues in contact with GLU 315 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A HIS* 3.5 34.4 + - - +
314A PRO* 1.3 77.4 - - - +
316A VAL* 1.3 73.2 + - + +
318A ALA* 3.3 6.7 + - - +
319A ARG* 3.1 52.0 + - - +
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Residues in contact with VAL 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 3.4 21.5 - - + -
313A HIS* 3.1 17.4 + - + +
315A GLU* 1.3 92.5 - - + +
317A ALA* 1.3 62.9 + - - +
318A ALA 3.2 0.5 + - - -
319A ARG 3.2 1.9 + - - -
320A VAL* 2.9 27.5 + - + +
344A TYR* 3.4 19.6 - - - +
348A VAL* 3.6 33.9 - - + -
404A PHE* 4.0 22.4 - - + -
406A PRO* 4.0 11.7 - - + -
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Residues in contact with ALA 317 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 3.6 38.0 - - + +
313A HIS 3.8 0.2 + - - -
314A PRO* 3.2 11.9 + - + +
316A VAL* 1.3 81.6 - - - +
318A ALA* 1.3 54.2 + - - +
320A VAL* 3.5 6.5 + - - +
321A GLN* 2.7 37.1 + - - +
450A LEU* 4.3 15.9 - - + +
455A LEU* 5.6 3.4 - - + -
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Residues in contact with ALA 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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314A PRO 3.0 16.4 + - - +
315A GLU* 3.6 8.1 - - - +
316A VAL 3.2 0.4 - - - -
317A ALA* 1.3 74.3 - - - +
319A ARG* 1.3 62.3 + - + +
321A GLN* 3.1 14.9 + - - +
322A GLU* 2.9 25.3 + - - +
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Residues in contact with ARG 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A GLU* 3.1 36.0 + - - +
318A ALA* 1.3 78.3 - - + +
320A VAL* 1.3 66.4 + - - +
322A GLU* 3.2 9.7 + - + +
323A GLU* 2.9 23.6 + - - +
344A TYR* 3.3 41.2 + - + -
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Residues in contact with VAL 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
310A LEU* 5.0 1.3 - - + -
316A VAL* 2.9 27.4 + - + +
317A ALA* 3.7 7.2 - - - +
319A ARG* 1.3 76.0 - - - +
321A GLN* 1.3 51.1 + - - +
323A GLU* 3.2 5.2 - - - +
324A ILE* 2.7 48.2 + - + +
344A TYR* 3.9 15.0 - - + -
345A THR* 3.5 30.9 + - + +
348A VAL* 4.0 19.5 - - + -
447A THR* 5.0 2.0 - - - +
450A LEU* 3.5 27.1 - - + -
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Residues in contact with GLN 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 ALA* 2.7 30.1 + - - +
318A ALA* 3.1 11.9 + - - +
320A VAL* 1.3 77.7 - - - +
322A GLU* 1.3 65.8 + - - +
324A ILE* 3.5 7.4 - - + +
325A GLU* 2.8 40.0 + - - +
450A LEU* 3.1 32.2 - - + +
451A GLN* 5.2 0.7 - - - -
453A PHE 3.0 25.3 - - - +
454A LYS* 4.3 7.1 - - - +
455A LEU 5.5 0.2 + - - -
487A ILE* 4.0 9.4 - - + +
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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 ALA 2.9 12.6 + - - +
319A ARG* 3.4 14.8 - - + +
321A GLN* 1.3 75.7 - - - +
323A GLU* 1.3 66.3 + - - +
325A GLU* 3.7 4.5 - - - +
326A ARG* 2.7 71.8 + - - +
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Residues in contact with GLU 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 ARG 2.9 9.0 + - - +
320A VAL* 3.2 10.3 - - - +
322A GLU* 1.3 87.8 + - - +
324A ILE* 1.3 61.0 + - - +
326A ARG* 3.5 23.0 + - - +
327A VAL* 3.1 34.4 + - + +
341A ARG 5.0 0.6 - - - +
342A MET* 3.1 31.1 - - + +
343A PRO* 4.1 7.1 - - - +
344A TYR* 2.8 27.5 + - + +
345A THR* 2.6 38.7 + - - +
415A ASN* 4.5 3.1 + - - -
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Residues in contact with ILE 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 VAL* 2.7 35.5 + - + +
321A GLN* 3.0 9.3 + - + +
323A GLU* 1.3 73.2 - - - +
325A GLU* 1.3 58.0 + - - +
328A ILE* 2.6 54.2 + - + +
329A GLY 4.6 1.1 - - - +
342A MET* 4.1 19.7 - - + -
447A THR* 3.2 32.1 - - - +
450A LEU* 3.9 22.9 - - + +
451A GLN* 3.7 32.8 - - + +
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Residues in contact with GLU 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLN* 2.8 30.6 + - - +
322A GLU* 3.8 5.6 - - - +
324A ILE* 1.3 81.0 - - - +
326A ARG* 1.3 60.0 + - - +
328A ILE 2.8 17.4 - - - +
329A GLY* 3.8 7.3 - - - +
330A ARG* 3.7 35.3 - - + +
451A GLN* 4.4 15.9 - - - +
487A ILE* 5.6 8.0 - - - +
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Residues in contact with ARG 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 GLU* 2.7 51.9 + - - +
323A GLU* 3.5 31.1 + - - +
325A GLU* 1.3 79.3 - - - +
327A VAL* 1.3 67.8 + - + +
341A ARG* 5.4 5.7 + - - +
415A ASN* 5.2 6.1 - - - +
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Residues in contact with VAL 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A GLU* 3.1 20.7 + - + +
326A ARG* 1.3 93.6 - - + +
328A ILE* 1.3 69.0 + - + +
329A GLY 4.3 0.2 + - - -
332A ARG* 4.1 9.2 + - - -
338A ASP* 4.3 12.6 - - + +
341A ARG* 3.8 35.4 - - + +
342A MET* 3.5 32.8 - - + -
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Residues in contact with ILE 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ILE* 2.6 29.1 + - + +
325A GLU 2.8 11.6 - - - +
327A VAL* 1.3 80.4 - - + +
329A GLY* 1.3 74.0 + - - +
332A ARG* 3.9 35.7 - - - +
333A SER 4.3 4.0 - - - +
334A PRO* 3.8 24.0 - - + -
338A ASP* 3.4 30.1 - - + +
342A MET* 3.6 27.8 - - + -
443A PHE* 4.9 0.4 - - + -
447A THR* 4.4 6.3 - - + -
451A GLN* 4.1 10.1 - - - +
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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