Contacts of the helix formed by residues 444 - 461 (chain A) in PDB entry 1TQN
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 GLY 444 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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137A PHE* 4.1 13.7 - - - -
442A CYS* 3.2 9.1 - - - -
443A ILE* 1.3 84.3 - - - +
445A MET* 1.3 51.1 + - - +
446A ARG* 3.4 2.5 - - - -
447A PHE* 3.1 6.7 + - - +
448A ALA* 2.7 36.7 + - - +
508A HEM 3.9 22.2 - - - +
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Residues in contact with MET 445 (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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435A PHE* 3.5 54.2 - - + -
441A ASN* 3.9 21.8 - - - +
442A CYS* 3.3 19.1 - - + +
443A ILE 3.4 2.8 - - - -
444A GLY* 1.3 75.5 - - - +
446A ARG* 1.3 61.8 + - + +
448A ALA* 3.1 2.8 + - - +
449A LEU* 2.8 45.8 + - + +
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Residues in contact with ARG 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A PHE* 3.6 24.2 - - + +
138A THR* 4.3 0.7 - - - +
139A SER* 3.6 27.3 - - - +
142A LEU* 3.5 18.8 - - + +
347A TYR* 3.5 18.4 + - - -
351A LEU* 5.4 7.1 - - - +
443A ILE 5.3 2.2 + - - +
444A GLY 3.4 0.6 - - - -
445A MET* 1.3 84.0 - - + +
447A PHE* 1.3 62.4 + - + +
449A LEU* 3.7 8.7 - - - +
450A MET* 2.8 32.4 + - - +
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Residues in contact with PHE 447 (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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137A PHE* 4.8 8.1 - - + -
142A LEU* 3.9 28.0 - - + -
145A MET* 4.3 11.2 - - + -
149A ILE* 4.4 8.4 - - + +
183A VAL* 4.0 21.3 - - + -
184A ILE* 6.2 2.0 - - + -
187A THR* 4.0 21.5 - - + -
271A PHE* 3.5 33.7 - + - -
444A GLY* 3.1 15.7 + - - +
446A ARG* 1.3 82.8 - - + +
448A ALA* 1.3 63.7 + - - +
450A MET* 3.6 1.4 - - - +
451A ASN* 2.8 44.7 + - + +
508A HEM 4.2 20.2 - - + -
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Residues in contact with ALA 448 (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 THR* 5.1 3.8 - - - +
435A PHE* 4.4 4.0 - - + -
444A GLY 2.7 20.3 + - - +
445A MET 3.5 4.9 - - - +
447A PHE* 1.3 79.4 - - - +
449A LEU* 1.3 61.6 + - - +
451A ASN* 3.5 4.3 - - - +
452A MET* 2.9 32.5 + - - +
508A HEM 3.9 47.3 - - + -
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Residues in contact with LEU 449 (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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357A ASP* 5.7 2.9 - - - +
360A VAL* 3.8 28.5 - - + -
361A ASN* 5.0 6.3 - - - +
364A LEU* 4.5 1.8 - - + -
435A PHE* 4.0 23.1 - - + -
445A MET* 2.8 42.6 + - + +
446A ARG* 3.7 7.9 - - - +
448A ALA* 1.3 71.7 - - - +
450A MET* 1.3 57.9 + - - +
452A MET* 3.8 7.3 - - + +
453A LYS* 2.9 52.4 + - + +
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Residues in contact with MET 450 (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 LEU* 4.1 23.6 - - + -
146A VAL* 4.2 7.6 - - + -
149A ILE* 4.3 2.5 - - + -
347A TYR* 3.2 50.3 - - + +
350A VAL* 3.7 21.8 - - + -
351A LEU* 4.1 18.6 - - + -
446A ARG 2.8 18.6 + - - +
447A PHE 3.6 3.6 - - - +
449A LEU* 1.3 76.8 - - - +
451A ASN* 1.3 62.3 + - - +
453A LYS* 3.9 3.8 - - - -
454A LEU* 3.0 52.1 + - + +
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Residues in contact with ASN 451 (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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149A ILE* 4.5 11.9 - - + +
179A TYR* 2.6 50.3 + - - -
180A SER* 5.3 2.4 + - - +
183A VAL* 3.6 28.5 - - - +
310A THR* 3.6 23.2 + - - +
447A PHE* 2.8 34.5 + - + +
448A ALA* 3.5 6.5 - - - +
450A MET* 1.3 74.1 - - - +
452A MET* 1.3 63.3 + - + +
454A LEU* 3.8 0.9 - - - +
455A ALA* 3.2 11.3 + - - +
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Residues in contact with MET 452 (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 THR* 3.7 25.1 - - + +
313A VAL* 3.3 39.0 - - + -
314A LEU* 3.6 18.8 - - + +
317A ILE* 4.9 2.0 - - + -
360A VAL* 4.5 9.4 - - + -
364A LEU* 4.7 3.4 - - + -
435A PHE* 4.7 0.4 - - + -
448A ALA* 2.9 25.4 + - + +
449A LEU* 3.9 22.0 - - + +
451A ASN* 1.3 78.4 - - - +
453A LYS* 1.3 58.4 + - + +
455A ALA* 3.3 4.5 + - - +
456A LEU* 2.8 37.7 + - + +
508A HEM 3.4 26.2 - - + -
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Residues in contact with LYS 453 (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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350A VAL* 3.5 33.3 + - + +
351A LEU* 5.2 11.1 + - + +
353A MET 5.2 0.6 + - - -
356A LEU* 3.5 26.5 - - + -
357A ASP* 2.7 48.1 + - - +
360A VAL* 4.2 18.4 - - + -
449A LEU* 2.9 36.9 + - - +
450A MET 3.9 0.9 - - - +
452A MET* 1.3 73.1 - - + +
454A LEU* 1.3 58.8 + - - +
456A LEU* 2.8 7.0 + - - +
457A ILE* 2.7 38.6 + - - +
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Residues in contact with LEU 454 (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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146A VAL* 3.9 17.9 - - + +
149A ILE* 3.4 38.6 - - + -
150A ALA* 4.7 13.2 - - + +
153A GLY* 5.5 1.3 - - - -
179A TYR* 4.6 4.3 - - - +
345A PRO* 3.4 37.6 - - + +
346A THR 4.4 0.4 - - - +
350A VAL* 3.6 16.8 - - + -
450A MET* 3.0 31.2 + - + +
451A ASN 3.8 4.3 - - - +
453A LYS* 1.3 75.4 - - - +
455A ALA* 1.3 61.7 + - - +
457A ILE* 3.6 5.7 + - - +
458A ARG* 3.1 27.0 + - - +
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Residues in contact with ALA 455 (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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153A GLY* 5.3 1.8 - - - -
156A LEU* 4.8 7.0 - - + -
176A PHE* 5.5 2.2 - - + -
179A TYR* 3.4 44.2 + - + +
314A LEU* 4.4 10.5 - - + -
451A ASN 3.2 4.2 + - - +
452A MET 3.5 8.3 - - - +
453A LYS 3.0 0.4 - - - -
454A LEU* 1.3 78.0 - - - +
456A LEU* 1.3 66.3 + - - +
458A ARG* 3.3 4.6 + - - +
459A VAL* 2.9 29.8 + - - +
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Residues in contact with LEU 456 (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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176A PHE* 5.4 2.7 - - + -
314A LEU* 3.6 18.2 - - + -
317A ILE* 3.9 38.6 - - + -
318A MET* 3.5 33.7 - - + -
321A LEU* 5.0 4.0 - - + -
331A LEU* 5.8 0.9 - - + -
335A ILE* 5.3 0.2 - - - -
356A LEU* 4.2 17.0 - - + -
359A VAL* 5.8 0.4 - - + -
360A VAL* 4.0 17.9 - - + -
452A MET 2.8 21.6 + - - +
453A LYS* 2.8 9.3 + - - +
455A ALA* 1.3 72.6 - - - +
457A ILE* 1.3 58.0 + - - +
459A VAL* 3.8 4.3 - - + +
460A LEU* 2.9 41.3 + - + +
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Residues in contact with ILE 457 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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335A ILE* 4.2 20.2 - - + +
339A LEU* 4.0 6.3 - - + -
345A PRO* 3.2 28.3 - - + -
350A VAL* 3.9 21.8 - - + -
353A MET* 3.3 35.0 - - + -
356A LEU* 3.8 23.1 - - + -
453A LYS 2.7 20.2 + - - +
454A LEU 3.7 3.4 - - - +
456A LEU* 1.3 70.7 - - - +
458A ARG* 1.3 61.7 + - - +
460A LEU* 4.0 0.3 - - - +
461A GLN* 2.8 49.3 + - - +
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Residues in contact with ARG 458 (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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150A ALA* 5.0 3.8 - - - +
153A GLY* 4.2 25.6 - - - +
154A ASP* 3.1 25.0 + - - +
157A VAL* 3.5 26.5 - - + +
342A LYS* 3.7 15.8 + - - +
344A PRO* 3.3 37.1 - - - +
345A PRO* 3.8 17.0 - - + +
454A LEU 3.1 15.8 + - - +
455A ALA* 3.7 3.4 - - - +
457A ILE* 1.3 81.1 - - - +
459A VAL* 1.3 65.4 + - + +
461A GLN* 3.1 32.7 + - - +
462A ASN* 3.6 25.0 + - - +
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Residues in contact with VAL 459 (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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156A LEU* 3.4 32.8 - - + -
157A VAL* 4.0 10.5 - - + -
160A LEU* 3.8 11.7 - - + -
176A PHE* 4.8 9.2 - - + -
318A MET* 5.1 3.4 - - + -
455A ALA 2.9 19.3 + - - +
456A LEU* 3.9 5.6 - - + +
458A ARG* 1.3 77.1 - - + +
460A LEU* 1.3 59.2 + - + +
462A ASN 3.0 3.8 + - - -
463A PHE* 2.9 33.5 + - + -
465A PHE* 3.1 41.5 - - + -
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Residues in contact with LEU 460 (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 MET* 4.3 20.9 - - + -
321A LEU* 3.9 11.4 - - + -
328A GLN* 3.8 33.7 - - + +
331A LEU* 3.4 42.4 - - + -
332A GLN* 3.5 10.9 + - + +
335A ILE* 3.8 14.8 - - + -
456A LEU* 2.9 29.1 + - + +
459A VAL* 1.3 69.0 - - + +
461A GLN* 1.3 56.3 + - - +
462A ASN 2.9 11.1 + - - -
463A PHE 3.7 9.0 - - - +
465A PHE* 4.6 2.0 - - + -
496A ARG* 3.0 27.5 + - - -
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Residues in contact with GLN 461 (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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335A ILE* 4.0 15.3 - - + +
336A ASP* 4.7 4.9 - - - +
339A LEU* 3.4 26.4 + - - +
342A LYS* 3.3 38.5 - - + +
343A ALA 2.9 27.0 + - - +
345A PRO* 4.3 0.7 - - - +
457A ILE* 2.8 25.2 + - - +
458A ARG* 3.1 40.4 + - - +
459A VAL 3.1 0.4 - - - -
460A LEU* 1.3 75.6 - - - +
462A ASN* 1.3 67.3 + - - +
496A ARG* 4.1 11.7 - - - +
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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