Contacts of the helix formed by residues 431 - 444 (chain B) 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 ALA 431 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17B TYR* 3.0 12.0 + - - +
68B PHE* 5.1 3.4 - - + -
69B THR* 4.1 18.8 - - + +
72B MET* 3.6 27.1 - - + +
73B LEU* 4.2 8.1 - - - +
427B THR 4.1 4.0 - - - +
428B ASP* 3.3 14.7 + - - +
430B ASN* 1.3 76.7 - - - +
432B GLY* 1.3 68.7 + - - +
434B SER* 3.3 2.4 + - - -
435B SER* 3.2 22.3 + - - -
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Residues in contact with GLY 432 (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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72B MET* 3.7 19.3 - - - +
320B ALA 4.2 6.7 - - - -
321B ASN* 3.4 27.2 + - - -
324B PHE* 3.6 4.9 - - - +
428B ASP 4.3 0.4 + - - -
429B TYR 4.9 0.2 + - - -
431B ALA* 1.3 78.0 - - - +
433B PHE* 1.3 57.2 + - - +
435B SER* 3.2 6.3 + - - -
436B ALA* 2.9 29.8 + - - +
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Residues in contact with PHE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 5.1 2.5 - - + -
13B SER* 4.6 3.6 - - - -
320B ALA* 4.0 18.5 - - + +
321B ASN* 4.5 0.2 + - - -
350B ILE* 4.1 28.9 - - + -
353B ALA* 4.3 20.6 - - + -
354B LEU* 3.8 12.6 - - + -
364B VAL* 3.7 31.4 - - + -
400B GLY 4.7 4.0 - - - -
402B LEU* 4.0 20.6 - - + -
429B TYR 3.8 19.1 + - - +
430B ASN* 3.8 22.8 - - - +
432B GLY* 1.3 75.2 - - - +
434B SER* 1.3 56.8 + - - +
436B ALA* 3.2 6.5 + - - +
437B LEU* 2.9 54.5 + - + +
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Residues in contact with SER 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 3.7 18.4 - - - +
13B SER* 2.6 24.4 + - - -
14B MET* 4.0 5.0 - - - +
17B TYR* 4.1 1.2 - - - -
73B LEU* 3.8 18.0 - - - +
84B TYR* 4.0 9.4 - - - -
430B ASN 2.5 24.5 + - - -
431B ALA 3.7 3.6 - - - -
433B PHE* 1.3 74.9 - - - +
435B SER* 1.3 58.5 + - - +
437B LEU* 3.1 8.9 + - - +
438B ALA* 2.9 25.6 + - - +
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Residues in contact with SER 435 (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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72B MET 2.8 26.2 + - - -
73B LEU* 4.1 4.3 + - - -
76B GLY* 3.4 16.1 - - - -
84B TYR* 4.8 2.1 + - - -
324B PHE* 3.5 32.9 - - - -
431B ALA 3.2 8.7 + - - -
432B GLY* 3.2 7.9 + - - -
434B SER* 1.3 76.5 - - - +
436B ALA* 1.3 62.1 + - - +
438B ALA* 3.3 7.5 + - - +
439B MET* 3.3 24.3 + - - +
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Residues in contact with ALA 436 (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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320B ALA 4.7 0.2 - - - +
324B PHE* 3.7 24.0 - - + +
327B LEU* 4.1 7.1 - - + +
350B ILE* 3.7 30.3 - - + -
432B GLY 2.9 12.7 + - - +
433B PHE* 3.4 9.2 - - - +
435B SER* 1.3 75.3 - - - +
437B LEU* 1.3 64.8 + - - +
439B MET* 3.0 9.8 + - - +
440B LEU* 3.0 25.3 + - - +
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Residues in contact with LEU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 4.0 21.8 - - + +
9B ALA* 3.8 17.0 - - + +
10B LEU* 3.7 35.7 - - + +
13B SER* 4.8 1.6 - - - -
350B ILE* 4.0 24.2 - - + -
354B LEU* 4.3 3.8 - - + -
433B PHE* 2.9 47.7 + - + +
434B SER* 3.1 11.6 + - - +
436B ALA* 1.3 77.1 - - - +
438B ALA* 1.3 56.5 + - - +
440B LEU* 3.2 5.3 + - + +
441B VAL* 2.9 35.9 + - - +
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Residues in contact with ALA 438 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B LEU* 4.0 12.1 - - + +
76B GLY 4.6 2.2 - - - +
80B SER* 3.0 25.6 + - - +
83B GLY* 3.2 16.8 - - - -
84B TYR* 3.7 36.8 - - + -
434B SER 2.9 9.1 + - - +
435B SER* 3.5 10.8 - - - +
436B ALA 3.2 0.2 - - - -
437B LEU* 1.3 75.2 - - - +
439B MET* 1.3 61.7 + - - +
441B VAL* 3.4 0.6 + - - -
442B GLU 3.3 6.2 + - - -
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Residues in contact with MET 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLY 5.4 0.4 - - - +
79B GLU* 4.1 19.5 - - + +
80B SER* 3.9 22.2 - - - -
324B PHE* 4.1 10.1 - - + -
327B LEU* 3.7 54.5 - - + +
328B VAL* 3.8 15.5 - - + +
331B LYS* 4.4 23.1 - - + +
435B SER 3.3 15.9 - - - +
436B ALA 3.0 7.1 + - - +
438B ALA* 1.3 76.6 - - - +
440B LEU* 1.3 64.1 + - + +
442B GLU* 3.3 7.1 + - - +
443B GLU* 3.1 23.1 + - - +
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Residues in contact with LEU 440 (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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6B TYR* 3.7 41.1 - - + +
327B LEU* 4.2 18.8 - - + -
347B VAL* 3.9 22.0 - - + -
350B ILE* 3.7 31.9 - - + -
436B ALA 3.0 15.0 + - - +
437B LEU* 3.2 7.2 + - - +
439B MET* 1.3 79.3 - - - +
441B VAL* 1.3 57.0 + - - +
443B GLU* 4.4 3.8 - - - +
444B TYR* 2.7 61.6 + - + +
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Residues in contact with VAL 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B TYR* 3.6 34.3 - - + +
7B ALA* 3.6 10.3 - - + +
10B LEU* 4.6 8.3 - - + -
83B GLY* 3.6 22.2 - - - +
86B ARG* 4.3 11.2 + - + +
87B SER* 4.2 13.9 - - - +
437B LEU 2.9 22.9 + - - +
438B ALA 3.8 5.2 - - - +
440B LEU* 1.3 75.9 - - - +
442B GLU* 1.3 60.7 + - - +
445B GLY* 2.7 44.7 + - - +
446B GLY 5.0 2.0 - - - +
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Residues in contact with GLU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B GLU 4.4 2.4 - - - +
80B SER* 3.0 38.7 + - - +
81B PRO* 5.1 0.7 - - - +
82B GLU* 3.4 27.7 - - + +
83B GLY* 4.0 7.4 - - - +
86B ARG* 3.7 25.4 + - - +
331B LYS* 3.5 23.3 + - - -
438B ALA 3.3 3.0 + - - -
439B MET* 3.5 10.5 - - - +
440B LEU 3.3 0.4 - - - -
441B VAL* 1.3 80.8 - - - +
443B GLU* 1.3 59.0 + - - +
445B GLY 4.8 0.3 + - - -
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Residues in contact with GLU 443 (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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327B LEU* 5.0 2.3 - - - +
343B HIS* 2.9 36.8 + - - -
439B MET 3.1 15.6 + - - +
440B LEU* 4.0 6.9 - - - +
442B GLU* 1.3 80.1 - - + +
444B TYR* 1.3 90.0 + - + +
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Residues in contact with TYR 444 (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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1B GLU* 4.0 15.8 - - - +
2B PRO* 3.5 25.4 - - + +
6B TYR* 3.8 25.1 - + + -
343B HIS* 3.1 25.5 - - - -
347B VAL* 4.0 16.6 - - + +
440B LEU* 2.7 44.9 + - + +
443B GLU* 1.3 100.1 + - + +
445B GLY* 1.3 60.0 + - - +
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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