Contacts of the helix formed by residues 427 - 444 (chain A) in PDB entry 1TF4
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 THR 427 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A PHE* 4.2 3.3 - - - -
17A TYR* 2.7 42.0 + - + -
20A GLN* 4.1 14.6 - - + +
53A TRP* 4.1 21.8 - - + -
54A TYR 3.3 16.6 - - - +
55A ASP* 2.9 34.1 + - - +
65A PRO 4.4 3.6 + - - -
66A MET* 4.6 6.9 - - + +
69A THR* 3.2 20.3 + - - +
426A ALA* 1.3 72.9 - - - +
428A ASP* 1.3 63.8 + - - +
429A TYR 3.4 0.7 + - - -
430A ASN 3.4 1.0 + - - -
431A ALA 3.5 0.2 + - - -
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Residues in contact with ASP 428 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASP* 5.1 0.7 + - - +
65A PRO* 4.7 7.3 - - + +
68A PHE* 4.6 16.9 - - + -
69A THR* 3.4 14.8 - - - +
206A TYR* 4.1 12.0 + - - -
260A TRP* 3.6 19.1 + - + +
317A ARG* 2.7 42.0 + - - +
321A ASN* 4.5 4.9 + - - +
426A ALA* 3.2 9.8 - - - +
427A THR* 1.3 78.7 + - - +
429A TYR* 1.3 76.9 + - - +
431A ALA* 3.3 17.1 + - - +
432A GLY 4.3 2.4 + - - -
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Residues in contact with TYR 429 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A TRP* 4.4 3.8 - - - +
314A GLY* 3.4 22.9 + - - -
317A ARG* 3.6 49.9 + - + +
320A ALA* 5.1 0.3 - - - +
321A ASN* 5.3 0.5 - - - +
402A LEU* 3.4 47.6 - - + +
403A VAL 4.2 5.6 - - - -
404A GLY* 3.8 14.0 - - - -
421A VAL 5.1 0.5 + - - -
424A GLU* 3.3 45.2 - - + +
425A VAL* 4.3 0.2 - - - -
426A ALA* 3.0 25.6 + - + +
428A ASP* 1.3 86.9 - - - +
430A ASN* 1.3 61.8 + - - +
431A ALA 3.8 0.3 + - - -
432A GLY 4.9 0.7 + - - -
433A PHE* 3.8 6.1 + - - +
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Residues in contact with ASN 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A SER* 2.9 20.2 + - - -
16A PHE* 3.7 21.2 - - + -
17A TYR* 3.0 23.5 + - + +
400A GLY 2.8 27.1 + - - -
401A ALA* 3.7 2.8 - - - -
402A LEU* 3.0 30.1 + - - +
426A ALA 3.6 0.7 + - - +
427A THR 3.4 1.6 + - - -
428A ASP 3.2 0.2 - - - -
429A TYR* 1.3 82.1 - - - +
431A ALA* 1.3 56.9 + - - +
432A GLY 3.8 0.2 - - - -
433A PHE* 4.1 10.0 - - - -
434A SER* 2.5 37.4 + - - -
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Residues in contact with ALA 431 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A TYR* 3.0 11.8 + - - +
68A PHE* 5.1 3.1 - - + -
69A THR* 4.1 22.4 - - + +
72A MET* 3.6 26.7 - - + -
73A LEU* 4.2 7.5 - - - +
321A ASN* 5.3 0.2 - - - +
427A THR 3.5 0.4 + - - +
428A ASP* 3.3 15.4 + - - +
429A TYR 3.4 0.2 - - - -
430A ASN* 1.3 75.8 - - - +
432A GLY* 1.3 67.6 + - - +
434A SER* 3.7 2.3 - - - -
435A SER* 3.2 23.6 + - - -
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Residues in contact with GLY 432 (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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72A MET* 3.7 18.7 - - - +
320A ALA 4.2 7.2 - - - -
321A ASN* 3.4 27.5 + - - -
324A PHE* 3.6 4.9 - - - +
428A ASP 4.3 0.6 + - - -
429A TYR 4.9 0.4 + - - -
431A ALA* 1.3 78.0 - - - +
433A PHE* 1.3 56.3 + - - +
435A SER* 3.2 6.6 + - - -
436A ALA* 2.9 29.6 + - - +
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Residues in contact with PHE 433 (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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9A ALA* 5.1 2.2 - - + -
13A SER* 4.6 3.6 - - - -
320A ALA* 4.0 18.4 - - + +
321A ASN* 4.5 0.2 + - - -
350A ILE* 4.1 28.0 - - + -
353A ALA* 4.3 13.9 - - + -
354A LEU* 3.8 12.6 - - + -
364A VAL* 3.7 31.9 - - + -
400A GLY 4.7 3.8 - - - -
402A LEU* 4.0 27.4 - - + -
429A TYR 3.8 19.4 + - - +
430A ASN* 3.8 23.5 - - - +
432A GLY* 1.3 74.7 - - - +
434A SER* 1.3 56.8 + - - +
436A ALA* 3.2 6.6 + - - +
437A LEU* 2.9 54.0 + - + +
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Residues in contact with SER 434 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A LEU* 3.6 16.8 - - - +
13A SER* 2.6 24.4 + - - -
14A MET* 4.0 5.4 - - - +
17A TYR* 4.1 2.8 - - - -
73A LEU* 3.8 16.4 - - - -
84A TYR* 3.9 9.6 + - - -
430A ASN 2.5 24.4 + - - -
431A ALA 3.7 3.6 - - - -
433A PHE* 1.3 75.2 - - - +
435A SER* 1.3 58.3 + - - +
437A LEU* 3.1 9.3 + - - +
438A ALA* 3.0 25.5 + - - +
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Residues in contact with SER 435 (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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72A MET 2.8 25.6 + - - -
73A LEU* 4.0 4.2 - - - -
76A GLY* 3.4 14.8 - - - -
84A TYR* 4.7 2.3 + - - -
324A PHE* 3.5 34.0 - - - -
431A ALA 3.2 8.7 + - - -
432A GLY* 3.2 8.1 + - - -
434A SER* 1.3 77.8 - - - +
436A ALA* 1.3 63.3 + - - +
438A ALA* 3.3 6.9 + - - +
439A MET* 3.3 24.4 + - - +
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Residues in contact with ALA 436 (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 4.7 0.4 - - - +
324A PHE* 3.7 23.5 - - + +
327A LEU* 4.1 7.1 - - + +
350A ILE* 3.7 30.3 - - + -
432A GLY 2.9 13.0 + - - +
433A PHE* 3.4 9.0 - - - +
435A SER* 1.3 76.5 - - - +
437A LEU* 1.3 63.5 + - - +
439A MET* 3.0 9.5 + - - +
440A LEU* 3.0 26.1 + - - +
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Residues in contact with LEU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A TYR* 4.1 21.7 - - + +
9A ALA* 3.8 16.6 - - + +
10A LEU* 3.7 36.3 - - + +
13A SER* 4.8 1.3 - - - -
350A ILE* 4.0 24.2 - - + -
354A LEU* 4.3 3.8 - - + -
433A PHE* 2.9 48.4 + - + +
434A SER* 3.1 11.9 + - - +
436A ALA* 1.3 77.8 - - - +
438A ALA* 1.3 55.8 + - - +
440A LEU* 3.2 4.9 + - + +
441A VAL* 2.9 36.0 + - - +
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Residues in contact with ALA 438 (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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10A LEU* 4.0 11.4 - - + +
76A GLY 4.5 2.2 - - - +
80A SER* 3.0 24.0 + - - +
83A GLY* 3.1 16.1 - - - -
84A TYR* 3.6 39.7 - - + +
434A SER 3.0 9.1 + - - +
435A SER* 3.5 11.0 - - - +
436A ALA 3.2 0.4 - - - -
437A LEU* 1.3 76.2 - - - +
439A MET* 1.3 61.5 + - - +
441A VAL* 3.4 0.8 + - - -
442A GLU 3.3 5.9 + - - -
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Residues in contact with MET 439 (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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76A GLY 5.8 0.2 - - - +
79A GLU* 4.1 26.5 - - - +
80A SER* 3.9 15.0 + - - -
324A PHE* 4.1 15.9 - - + -
327A LEU* 3.5 52.3 - - + +
328A VAL* 4.2 4.3 - - - +
331A LYS* 3.9 29.2 - - + +
435A SER 3.3 15.9 - - - +
436A ALA 3.0 7.0 + - - +
438A ALA* 1.3 76.7 - - - +
440A LEU* 1.3 63.4 + - - +
442A GLU* 3.2 7.1 + - - +
443A GLU* 3.1 22.6 + - - +
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Residues in contact with LEU 440 (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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6A TYR* 3.7 41.1 - - + +
327A LEU* 4.2 17.9 - - + -
347A VAL* 3.9 21.5 - - + -
350A ILE* 3.8 31.9 - - + -
351A ASN* 5.2 0.2 - - - +
436A ALA 3.0 17.0 + - - +
437A LEU* 3.7 7.9 - - - +
439A MET* 1.3 76.0 - - - +
441A VAL* 1.3 59.2 + - - +
443A GLU* 4.4 4.7 - - - +
444A TYR* 2.7 59.0 + - + +
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Residues in contact with VAL 441 (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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6A TYR* 3.6 10.3 - - + +
7A ALA* 3.6 34.8 - - + +
10A LEU* 4.5 6.3 - - + -
83A GLY* 3.5 24.2 - - - +
86A ARG* 4.3 11.6 + - + +
87A SER* 4.1 14.1 - - - +
437A LEU 2.9 23.4 + - - +
438A ALA 3.8 5.6 - - - +
439A MET 3.3 0.2 - - - -
440A LEU* 1.3 77.1 - - - +
442A GLU* 1.3 59.3 + - - +
445A GLY* 2.7 43.1 + - - +
446A GLY 5.0 1.6 - - - +
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Residues in contact with GLU 442 (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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79A GLU 4.4 2.5 - - - +
80A SER* 3.0 37.7 + - - +
81A PRO* 4.7 1.2 - - - +
82A GLU* 3.6 26.7 - - + +
83A GLY* 3.9 6.9 - - - +
86A ARG* 3.6 24.9 + - - +
331A LYS* 3.5 23.8 + - - -
438A ALA 3.3 2.2 + - - +
439A MET* 3.2 11.2 + - - +
441A VAL* 1.3 81.9 - - - +
443A GLU* 1.3 59.3 + - - +
445A GLY 4.8 0.3 + - - -
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A LEU* 5.1 1.9 - - - +
343A HIS* 2.9 36.8 + - - -
439A MET 3.1 14.2 + - - +
440A LEU* 4.1 6.8 - - - +
442A GLU* 1.3 79.9 - - - +
444A TYR* 1.3 89.6 + - + +
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Residues in contact with TYR 444 (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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1A GLU* 3.9 18.0 - - - +
2A PRO* 3.6 24.3 - - + +
6A TYR* 3.9 24.7 - + + -
343A HIS* 3.2 25.3 - - - -
347A VAL* 4.0 16.2 - - + +
440A LEU* 2.7 46.0 + - + +
443A GLU* 1.3 99.7 + - + +
445A GLY* 1.3 59.9 + - - +
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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
------------------------------------------------------------
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