Contacts of the helix formed by residues 399 - 417 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A SER* 3.0 30.1 + - - -
14A ARG* 4.8 4.6 - - - +
206A VAL* 4.3 2.9 - - - -
207A GLY 3.0 19.7 + - - -
208A ASP* 3.3 19.4 + - - +
210A GLY* 3.4 27.8 - - - +
398A CYS* 1.3 81.4 - - - +
400A SER* 1.3 60.8 + - - +
401A GLU* 2.7 34.5 + - - +
402A ARG* 2.9 21.2 + - + +
403A LEU* 3.1 6.7 - - - +
13B SER 2.9 16.5 + - - -
206B VAL* 3.6 23.0 - - - +
398B CYS* 3.5 11.7 - - - -
399B ARG* 3.5 34.9 - - - +
401B GLU* 3.6 8.7 - - - +
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Residues in contact with SER 400 (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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376A GLU* 5.4 0.9 - - - -
399A ARG* 1.3 67.8 - - - +
401A GLU* 1.3 56.3 + - - +
402A ARG 2.8 5.8 - - - -
403A LEU* 3.7 9.7 - - - +
404A ALA* 2.9 30.8 + - - +
11B LEU 5.4 0.2 + - - -
12B ASP 4.4 1.0 - - - -
13B SER* 3.5 18.2 + - - -
374B GLU 3.8 3.5 + - - -
375B THR* 3.8 5.2 - - - -
376B GLU* 4.2 20.6 + - - +
400B SER* 4.5 2.9 - - - -
401B GLU* 2.9 43.7 + - - +
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Residues in contact with GLU 401 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 3.4 12.9 - - - -
374A GLU* 3.6 12.5 - - + +
375A THR 3.6 16.8 - - - +
376A GLU* 5.1 0.4 - - - +
394A THR* 4.6 0.2 + - - -
399A ARG* 2.7 41.6 + - - +
400A SER* 1.3 71.1 - - - +
402A ARG* 1.3 104.3 + - - +
404A ALA* 4.7 0.4 - - - -
405A LYS* 2.9 32.3 + - - +
399B ARG* 3.8 0.2 - - - -
400B SER* 3.0 41.4 + - - +
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Residues in contact with ARG 402 (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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13A SER* 3.4 9.9 + - - -
208A ASP 2.9 17.7 + - - -
209A GLU* 3.9 15.7 - - - +
370A HIS* 2.7 34.6 + - - -
371A ARG 2.9 16.2 + - - -
372A SER 2.6 26.8 + - - -
374A GLU* 3.4 6.6 - - - +
394A THR* 3.2 23.0 - - - +
395A GLY* 3.8 6.7 - - - -
396A ALA 3.4 19.3 - - - +
398A CYS 3.2 20.4 - - - +
399A ARG 2.9 6.4 + - - +
400A SER 2.8 0.4 - - - -
401A GLU* 1.3 106.4 + - + +
403A LEU* 1.3 65.7 + - - +
404A ALA 3.1 1.3 - - - -
405A LYS* 3.0 17.7 + - - +
406A TYR* 3.3 15.2 + - + -
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Residues in contact with LEU 403 (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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181A MET* 4.6 1.8 - - + -
397A PRO* 3.7 26.0 - - + +
398A CYS* 3.7 9.2 - - - +
399A ARG 3.1 44.7 + - - +
400A SER* 3.6 8.7 + - - +
402A ARG* 1.3 78.7 - - - +
404A ALA* 1.3 54.1 + - - +
406A TYR* 4.1 11.0 - - + -
407A ASN* 2.6 50.4 + - - +
11B LEU* 3.8 29.8 - - + +
12B ASP 3.3 25.8 - - - +
13B SER* 4.0 2.9 - - - -
376B GLU* 4.9 0.4 - - - +
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Residues in contact with ALA 404 (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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376A GLU* 4.2 14.8 - - - +
378A THR* 3.3 29.4 - - + +
400A SER 2.9 21.2 + - - +
401A GLU 4.7 0.9 - - - +
402A ARG 3.1 0.2 + - - -
403A LEU* 1.3 76.4 - - - +
405A LYS* 1.3 66.3 + - + +
407A ASN* 4.0 1.2 - - - +
408A GLN* 3.1 17.3 + - - +
411A ARG* 4.5 1.4 + - - -
376B GLU* 3.6 30.7 + - + +
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Residues in contact with LYS 405 (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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374A GLU* 2.7 35.5 + - - -
375A THR 2.9 11.7 + - - -
377A ASP* 2.8 28.1 + - - +
378A THR* 4.2 9.9 - - - +
380A ILE* 3.6 30.7 - - + -
381A ALA* 3.7 6.5 - - + +
392A ILE* 5.6 0.2 - - + -
394A THR* 3.6 24.5 - - + +
401A GLU 2.9 26.3 + - - +
402A ARG 3.0 7.7 + - - +
404A ALA* 1.3 76.4 - - + +
406A TYR* 1.3 65.5 + - - +
408A GLN* 3.2 6.9 + - - +
409A LEU* 2.9 29.1 + - + +
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Residues in contact with TYR 406 (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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147A PRO* 3.8 13.9 - - + -
148A ALA 3.7 6.4 + - - -
149A PHE* 3.4 26.1 - + - -
177A PHE* 3.6 15.6 - + - -
181A MET* 3.4 35.2 - - + -
392A ILE* 5.1 2.0 - - + -
393A LYS* 4.6 0.2 - - - -
394A THR* 3.2 44.6 + - + -
395A GLY 2.5 30.3 + - - -
396A ALA 3.8 9.0 - - - -
397A PRO* 4.8 0.2 - - + -
402A ARG 3.3 18.3 + - - -
403A LEU* 3.1 16.0 + - + +
405A LYS* 1.3 76.7 - - - +
407A ASN* 1.3 64.1 + - - +
409A LEU* 3.2 10.5 + - + +
410A MET* 3.1 22.5 + - - +
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Residues in contact with ASN 407 (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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403A LEU* 2.6 26.4 + - - +
404A ALA 4.0 0.7 - - - +
406A TYR* 1.3 72.1 - - - +
408A GLN* 1.3 63.2 + - - +
410A MET* 3.2 18.6 + - - +
411A ARG* 3.1 36.6 + - - +
10B ILE* 3.3 20.4 - - + +
11B LEU* 3.0 44.6 + - - +
376B GLU* 3.0 34.6 + - - +
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Residues in contact with GLN 408 (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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378A THR* 4.0 17.8 + - - +
381A ALA* 3.5 22.0 - - + -
382A ASP* 2.9 27.9 + - - +
404A ALA 3.1 19.3 + - - +
405A LYS 3.2 4.9 + - - +
407A ASN* 1.3 78.3 - - - +
409A LEU* 1.3 57.3 + - - +
411A ARG* 3.0 34.8 + - - +
412A ILE* 2.9 37.4 + - + +
31B ARG* 4.8 3.5 + - - -
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Residues in contact with LEU 409 (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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144A LEU* 3.6 9.9 - - + +
145A PRO* 4.2 7.9 - - + -
177A PHE* 3.3 44.2 - - + -
381A ALA* 3.5 32.3 - - + +
384A VAL* 3.9 6.7 - - + -
385A VAL* 3.7 19.3 - - + -
392A ILE* 4.1 25.8 - - + -
394A THR* 5.4 0.2 - - + -
405A LYS* 2.9 21.1 + - + +
406A TYR* 3.2 9.2 + - + +
408A GLN* 1.3 76.9 - - - +
410A MET* 1.3 62.9 + - - +
412A ILE* 3.2 5.9 + - + +
413A GLU* 3.0 18.9 + - - +
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Residues in contact with MET 410 (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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177A PHE* 3.8 14.8 - - + -
178A ARG* 3.1 49.3 + - + +
181A MET* 3.9 24.5 - - + -
406A TYR 3.1 11.9 + - - +
407A ASN* 3.4 35.4 - - - +
409A LEU* 1.3 76.7 - - - +
411A ARG* 1.3 62.7 + - + +
413A GLU* 3.3 1.3 + - - -
414A GLU* 3.0 19.8 + - - +
8B ARG* 5.6 6.5 - - - -
9B GLU 3.9 23.3 - - - +
10B ILE* 4.0 6.5 - - + -
11B LEU* 4.3 12.1 - - + +
56B TYR* 5.6 2.0 - - - -
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Residues in contact with ARG 411 (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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378A THR* 5.5 2.4 - - - +
404A ALA 4.5 2.6 + - - -
407A ASN* 3.1 23.2 + - - +
408A GLN* 3.0 47.1 + - - +
410A MET* 1.3 72.6 - - - +
412A ILE* 1.3 60.6 + - - +
414A GLU* 3.3 8.9 + - - +
415A GLU* 2.9 29.1 + - - +
8B ARG* 3.9 24.2 - - - +
10B ILE* 4.9 0.2 - - - +
20B GLU* 2.7 39.5 + - - -
31B ARG* 3.6 38.9 - - - +
376B GLU* 3.5 23.8 + - - +
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Residues in contact with ILE 412 (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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130A TYR* 3.6 32.8 - - + -
144A LEU* 4.8 1.3 - - + -
381A ALA 3.9 20.0 - - - +
382A ASP* 3.9 16.6 - - - +
385A VAL* 4.0 17.5 - - + -
408A GLN* 2.9 39.4 + - + +
409A LEU* 3.5 16.8 - - + +
411A ARG* 1.3 74.6 - - - +
413A GLU* 1.3 66.7 + - - +
415A GLU* 3.2 3.9 + - - +
416A LEU* 2.9 38.9 + - + +
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Residues in contact with GLU 413 (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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144A LEU* 3.8 29.3 - - + +
176A SER* 3.4 12.3 + - - -
177A PHE* 2.7 29.3 + - + +
178A ARG* 2.9 51.3 + - - +
409A LEU 3.0 12.5 + - - +
410A MET* 3.6 8.1 - - - +
411A ARG 3.3 0.2 - - - -
412A ILE* 1.3 76.4 - - - +
414A GLU* 1.3 58.7 + - - +
416A LEU* 3.3 2.9 + - - +
417A GLY* 2.9 31.5 + - - +
420A ALA* 5.8 1.1 - - + +
421A ARG 6.0 0.2 - - - -
422A PHE* 4.9 2.6 + - - +
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Residues in contact with GLU 414 (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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178A ARG* 3.2 25.6 + - - +
410A MET 3.0 11.0 + - - +
411A ARG* 3.5 8.5 - - - +
413A GLU* 1.3 78.3 - - - +
415A GLU* 1.3 62.1 + - - +
417A GLY* 3.5 9.4 + - - -
6B TRP* 3.3 29.4 + - + +
8B ARG* 2.9 49.0 + - - +
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Residues in contact with GLU 415 (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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128A PRO* 3.5 14.7 - - - +
130A TYR* 2.7 37.8 + - - +
411A ARG 2.9 16.9 + - - +
412A ILE* 3.2 5.2 + - - +
414A GLU* 1.3 79.4 - - - +
416A LEU* 1.3 60.7 + - - +
417A GLY* 4.7 0.2 - - - -
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Residues in contact with LEU 416 (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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130A TYR* 3.7 29.6 - - + +
131A ARG* 4.1 17.3 - - - +
142A LEU* 4.3 7.2 - - + -
144A LEU* 4.1 8.3 - - + -
385A VAL* 4.3 9.4 - - + -
412A ILE* 2.9 36.6 + - + +
413A GLU 3.9 3.1 - - - +
415A GLU* 1.3 77.6 - - - +
417A GLY* 1.3 59.0 + - - +
418A ASP 3.1 0.9 + - - -
419A GLU* 2.8 46.7 + - + +
420A ALA* 3.4 31.4 - - + +
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Residues in contact with GLY 417 (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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413A GLU* 2.9 20.5 + - - +
414A GLU* 3.5 7.5 + - - -
415A GLU 3.4 3.2 - - - -
416A LEU* 1.3 74.8 - - - +
418A ASP* 1.3 58.2 + - - -
419A GLU 3.3 3.1 + - - -
420A ALA* 3.7 13.9 + - - +
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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