Contacts of the helix formed by residues 399 - 417 (chain B) in PDB entry 1TE6
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 ARG 399 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A SER 2.8 17.5 + - - -
206A VAL* 3.8 20.2 - - - +
398A CYS* 3.7 11.1 - - - -
399A ARG* 3.5 35.6 - - - +
401A GLU* 3.8 6.7 - - - +
13B SER* 3.0 29.5 + - - -
14B ARG* 4.7 4.0 - - - +
206B VAL* 4.3 3.8 - - - -
207B GLY 2.8 26.1 + - - -
208B ASP* 3.2 21.2 + - - +
210B GLY* 3.4 26.0 - - - +
398B CYS* 1.3 80.7 - - - +
400B SER* 1.3 60.4 + - - +
401B GLU* 2.8 34.3 + - - +
402B ARG* 2.9 20.1 + - + +
403B LEU* 3.2 10.2 + - - +
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Residues in contact with SER 400 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU 5.3 0.2 + - - -
12A ASP 4.4 1.2 - - - -
13A SER* 3.5 15.8 + - - -
374A GLU 3.7 5.9 + - - -
375A THR* 3.9 12.8 - - - -
376A GLU* 4.4 10.9 + - - +
400A SER* 4.5 2.7 - - - -
401A GLU* 3.0 43.6 + - - +
376B GLU* 5.3 0.9 - - - -
399B ARG* 1.3 66.7 - - - +
401B GLU* 1.3 56.3 + - - +
402B ARG 2.8 5.8 - - - -
403B LEU* 3.7 10.6 - - - +
404B ALA* 2.8 31.0 + - - +
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Residues in contact with GLU 401 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399A ARG* 3.6 0.9 - - - -
400A SER* 2.9 41.5 + - - +
13B SER* 3.1 14.3 - - - -
374B GLU* 3.6 11.0 - - + +
375B THR 3.6 16.8 - - - +
376B GLU* 5.0 0.2 - - - +
394B THR* 4.5 0.2 + - - -
399B ARG* 2.8 43.5 + - - +
400B SER* 1.3 72.8 - - - +
402B ARG* 1.3 104.6 + - - +
404B ALA* 4.9 0.4 - - - -
405B LYS* 2.9 31.3 + - - +
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Residues in contact with ARG 402 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B SER* 3.4 4.8 + - - -
208B ASP 3.1 15.7 + - - -
209B GLU* 4.0 12.0 - - - +
370B HIS* 2.7 36.3 + - - -
371B ARG 3.0 16.3 + - - -
372B SER 2.8 25.3 + - - -
374B GLU* 3.6 6.3 - - - +
394B THR 3.1 24.6 - - - +
395B GLY* 3.8 7.6 - - - -
396B ALA 3.5 19.1 - - - +
398B CYS 3.5 12.8 - - - +
399B ARG* 2.9 13.2 + - + +
400B SER 2.8 0.4 - - - -
401B GLU* 1.3 116.9 + - + +
403B LEU* 1.3 65.2 + - - +
404B ALA 3.1 1.1 - - - -
405B LYS* 3.0 18.7 + - - +
406B TYR* 3.4 15.7 + - + -
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Residues in contact with LEU 403 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 3.8 31.6 - - + +
12A ASP 3.4 23.8 - - - +
13A SER* 4.3 0.2 - - - -
376A GLU* 5.1 0.4 - - - +
181B MET* 4.4 2.7 - - + -
397B PRO* 3.5 21.5 - - + +
398B CYS* 3.3 28.0 - - - +
399B ARG 3.2 29.0 + - - +
400B SER* 4.0 10.1 - - - +
402B ARG* 1.3 76.8 - - - +
404B ALA* 1.3 60.7 + - - +
406B TYR* 4.1 12.8 - - + -
407B ASN* 2.7 45.3 + - - +
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Residues in contact with ALA 404 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376A GLU* 3.7 28.9 + - + +
376B GLU* 3.9 17.0 - - - +
378B THR* 3.4 23.6 - - + +
400B SER* 2.8 25.2 + - - +
401B GLU 4.8 0.4 - - - -
402B ARG 3.1 0.2 + - - -
403B LEU* 1.3 72.8 - - - +
405B LYS* 1.3 67.4 + - + +
407B ASN* 4.1 1.2 - - - +
408B GLN* 3.1 24.6 + - - +
411B ARG* 4.5 0.9 + - - -
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Residues in contact with LYS 405 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B GLU* 2.6 34.6 + - - -
375B THR 2.9 17.0 + - - -
377B ASP* 2.8 28.6 + - - +
378B THR* 4.3 6.5 - - - -
380B ILE* 3.5 31.2 - - + -
381B ALA* 3.6 11.6 - - + +
392B ILE* 5.5 0.7 - - + -
394B THR* 3.4 26.2 - - + +
401B GLU 2.9 21.6 + - - +
402B ARG 3.0 7.2 + - - +
404B ALA* 1.3 74.5 - - + +
406B TYR* 1.3 60.5 + - - +
408B GLN* 3.2 4.8 + - - +
409B LEU* 2.9 34.8 + - + +
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Residues in contact with TYR 406 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B PRO* 3.8 14.4 - - + -
148B ALA 3.6 7.1 + - - -
149B PHE* 3.5 20.8 - + - -
177B PHE* 3.5 15.8 - + - -
181B MET* 3.4 38.8 - - + -
392B ILE* 4.9 4.7 - - + -
393B LYS* 4.4 0.2 - - - -
394B THR* 3.1 46.6 + - + -
395B GLY 2.6 30.6 + - - -
396B ALA 3.8 7.9 - - - -
402B ARG 3.4 17.4 + - - -
403B LEU* 3.2 16.9 + - + +
405B LYS* 1.3 80.2 - - - +
407B ASN* 1.3 60.7 + - - +
409B LEU* 3.2 9.7 + - + +
410B MET* 3.0 21.5 + - - +
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Residues in contact with ASN 407 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.7 18.6 - - + +
11A LEU* 3.0 44.2 + - - +
376A GLU* 3.2 31.1 + - - +
403B LEU* 2.7 28.7 + - - +
404B ALA 4.1 0.2 - - - +
406B TYR* 1.3 73.7 - - - +
408B GLN* 1.3 62.3 + - - +
410B MET* 3.0 22.2 + - - +
411B ARG* 3.0 35.6 + - - +
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Residues in contact with GLN 408 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ARG* 4.8 4.0 + - - -
378B THR* 3.9 18.7 + - - +
381B ALA* 3.5 21.8 - - + -
382B ASP* 2.9 29.6 + - - +
404B ALA 3.1 19.7 + - - +
405B LYS 3.2 5.3 + - - +
407B ASN* 1.3 78.1 - - - +
409B LEU* 1.3 57.0 + - - +
411B ARG* 3.1 32.3 + - - +
412B ILE* 2.9 45.8 + - + +
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Residues in contact with LEU 409 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LEU* 3.7 6.8 - - + +
145B PRO* 4.2 7.4 - - + -
177B PHE* 3.3 41.7 - - + -
381B ALA* 3.4 34.1 - - + +
384B VAL* 3.9 7.4 - - + -
385B VAL* 3.6 21.3 - - + -
392B ILE* 4.2 24.7 - - + -
405B LYS* 2.9 22.3 + - + +
406B TYR* 3.5 6.3 - - + +
407B ASN 3.2 0.2 - - - -
408B GLN* 1.3 76.3 - - - +
410B MET* 1.3 62.4 + - - +
412B ILE* 3.3 6.0 + - + +
413B GLU* 3.0 23.6 + - - +
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Residues in contact with MET 410 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 5.8 4.5 - - - -
9A GLU 4.3 9.9 - - - +
10A ILE* 4.1 18.4 - - + -
11A LEU* 4.2 12.1 - - + +
56A TYR* 5.3 3.1 - - - -
177B PHE* 3.9 14.6 - - + -
178B ARG* 3.3 45.6 + - + +
181B MET* 3.9 24.9 - - + -
406B TYR 3.0 13.0 + - - +
407B ASN* 3.0 41.5 + - - +
409B LEU* 1.3 77.9 - - - +
411B ARG* 1.3 57.7 + - + +
413B GLU* 3.2 1.4 + - - -
414B GLU* 2.9 26.1 + - - +
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Residues in contact with ARG 411 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A ARG* 4.1 21.8 - - - +
10A ILE* 4.5 1.4 - - + +
20A GLU* 2.7 40.1 + - - -
31A ARG* 3.5 38.6 - - - +
376A GLU* 3.2 27.3 + - - +
378B THR* 5.4 3.0 - - - +
404B ALA 4.5 1.4 + - - -
407B ASN* 3.0 26.6 + - - +
408B GLN* 3.1 48.1 + - - +
410B MET* 1.3 77.0 - - - +
412B ILE* 1.3 59.4 + - + +
414B GLU* 3.3 9.8 + - - +
415B GLU* 2.8 28.6 + - - +
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Residues in contact with ILE 412 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B PRO* 5.7 0.7 - - + -
130B TYR* 3.2 47.6 - - + -
144B LEU* 4.7 1.8 - - + -
382B ASP* 3.8 14.4 - - - +
385B VAL* 4.0 31.6 - - + -
408B GLN* 2.9 39.6 + - + +
409B LEU* 3.6 8.7 - - + +
411B ARG* 1.3 75.1 - - + +
413B GLU* 1.3 66.5 + - - +
415B GLU* 3.0 8.0 + - + +
416B LEU* 2.9 31.9 + - + +
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Residues in contact with GLU 413 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144B LEU* 3.9 25.1 - - + +
176B SER* 3.4 12.4 - - - -
177B PHE* 2.7 29.9 + - + +
178B ARG* 2.9 51.1 + - - +
409B LEU 3.0 13.2 + - - +
410B MET* 3.5 8.1 - - - +
412B ILE* 1.3 76.6 - - - +
414B GLU* 1.3 63.1 + - - +
416B LEU* 3.2 13.2 + - - +
417B GLY* 3.4 9.0 + - - +
420B ALA* 3.7 18.7 - - + +
421B ARG 5.5 0.7 - - - -
422B PHE* 4.8 3.3 + - - +
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Residues in contact with GLU 414 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A TRP* 3.2 26.9 + - + +
8A ARG* 2.8 53.0 + - - +
178B ARG* 3.3 27.6 + - - +
410B MET 2.9 12.1 + - - +
411B ARG* 3.4 9.0 - - - +
413B GLU* 1.3 77.5 - - - +
415B GLU* 1.3 64.6 + - - +
417B GLY* 3.2 13.7 + - - -
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Residues in contact with GLU 415 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B PRO* 5.6 5.2 - - + +
130B TYR* 3.3 23.9 + - + +
411B ARG 2.8 20.0 + - - +
412B ILE* 3.0 9.8 + - + +
414B GLU* 1.3 78.3 - - - +
416B LEU* 1.3 60.7 + - - +
417B GLY* 3.3 1.2 + - - -
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Residues in contact with LEU 416 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B TYR* 3.8 13.0 - - + +
131B ARG* 3.4 38.6 - - - +
142B LEU* 4.4 21.3 - - + +
144B LEU* 3.6 29.8 - - + -
385B VAL* 4.7 1.8 - - + -
412B ILE* 2.9 24.9 + - + +
413B GLU 3.2 6.0 + - - +
415B GLU* 1.3 76.0 - - - +
417B GLY* 1.3 65.0 + - - +
418B ASP 3.3 0.5 + - - -
419B GLU* 3.1 30.7 + - + +
420B ALA* 3.7 17.7 - - + +
421B ARG 5.3 0.4 - - - +
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Residues in contact with GLY 417 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413B GLU 3.4 4.4 + - - +
414B GLU 3.2 12.0 + - - -
415B GLU 3.1 5.5 - - - -
416B LEU* 1.3 77.2 - - - +
418B ASP* 1.3 62.2 + - - -
420B ALA* 3.2 19.1 - - - +
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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
------------------------------------------------------------
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